C8855 Advanced Molecular Modelling Methods
Faculty of ScienceSpring 2024
- Extent and Intensity
- 1/0/0. 1 credit(s) (plus extra credits for completion). Recommended Type of Completion: k (colloquium). Other types of completion: zk (examination).
- Teacher(s)
- RNDr. Petr Kulhánek, Ph.D. (lecturer)
- Guaranteed by
- RNDr. Petr Kulhánek, Ph.D.
National Centre for Biomolecular Research – Faculty of Science
Contact Person: RNDr. Petr Kulhánek, Ph.D.
Supplier department: National Centre for Biomolecular Research – Faculty of Science - Timetable
- Mon 19. 2. to Sun 26. 5. Wed 9:00–9:50 C04/118
- Prerequisites
- Basic level of general and physical chemistry. A basic knowledge of quantum chemistry is an advantage. It is strongly suggested that the student go first through the courses C7790 Introduction to Molecular Modelling or C9087 Computational Chemistry for Structural Biology.
- Course Enrolment Limitations
- The course is also offered to the students of the fields other than those the course is directly associated with.
- fields of study / plans the course is directly associated with
- Macromolecular Chemistry (programme PřF, D-CH) (2)
- Organic Chemistry (programme PřF, N-CH)
- Course objectives
- The course is aimed at acquiring advanced knowledge in the field of computational chemistry. Its orientation is strongly application-oriented. The course will discuss the methods needed to build models for simulations of predominantly biomolecular systems. Basic problems of incomplete experimental structures and the appropriateness of using artificial intelligence tools to predict structures will be discussed. The preparation of pre-reaction complexes for studying enzymatic reactions and basic methods for studying reaction mechanisms will also be discussed.
- Learning outcomes
- The student will gain advanced knowledge to study the dynamics and reactivity of biomolecular systems using molecular modelling tools.
- Syllabus
- Basic requirements for models of biomolecular systems * Limitation of experimental (X-ray, NMR, CryoEM) and predicted (AlphaFold2, ESM-Fold, RoseTTAFold2) structures * Ionizable groups and the effect of pH on the model * Docking of substrates into the active site * How to solvate biomolecular systems correctly * Types of water and ion models * Molecular dynamics (MD) of biomolecular systems * Analysis of MD trajectories * Hybrid QM/MM description of the active site of an enzymatic reaction * Calculation of reaction profiles * Study of reaction mechanisms
- Literature
- Encyclopedia of computational chemistry. Edited by Paul von R. Schleyer. Chichester: John Wiley & sons, 1998, xxix, 812. ISBN 047196588X. info
- LEACH, Andrew R. Molecular modelling : principles and applications. 2nd ed. Harlow: Prentice Hall, 2001, xxiii, 744. ISBN 0582382106. info
- JENSEN, Frank. Introduction to computational chemistry. Third edition. Chichester: Wiley, 2017, xxii, 638. ISBN 9781118825990. info
- Teaching methods
- Lectures combined with discussions.
- Assessment methods
- The course ends with a written test followed by an optional oral examination.
- Language of instruction
- Czech
- Further Comments
- Study Materials
The course can also be completed outside the examination period.
The course is taught annually.
C8855 Advanced Molecular Modelling Methods
Faculty of ScienceSpring 2025
- Extent and Intensity
- 1/0/0. 1 credit(s) (plus extra credits for completion). Recommended Type of Completion: k (colloquium). Other types of completion: zk (examination).
- Teacher(s)
- RNDr. Petr Kulhánek, Ph.D. (lecturer)
- Guaranteed by
- RNDr. Petr Kulhánek, Ph.D.
National Centre for Biomolecular Research – Faculty of Science
Contact Person: RNDr. Petr Kulhánek, Ph.D.
Supplier department: National Centre for Biomolecular Research – Faculty of Science - Prerequisites
- Basic level of general and physical chemistry. A basic knowledge of quantum chemistry is an advantage. It is strongly suggested that the student go first through the courses C7790 Introduction to Molecular Modelling or C9087 Computational Chemistry for Structural Biology.
- Course Enrolment Limitations
- The course is also offered to the students of the fields other than those the course is directly associated with.
- fields of study / plans the course is directly associated with
- Macromolecular Chemistry (programme PřF, D-CH) (2)
- Organic Chemistry (programme PřF, N-CH)
- Course objectives
- The course is aimed at acquiring advanced knowledge in the field of computational chemistry. Its orientation is strongly application-oriented. The course will discuss the methods needed to build models for simulations of predominantly biomolecular systems. Basic problems of incomplete experimental structures and the appropriateness of using artificial intelligence tools to predict structures will be discussed. The preparation of pre-reaction complexes for studying enzymatic reactions and basic methods for studying reaction mechanisms will also be discussed.
- Learning outcomes
- The student will gain advanced knowledge to study the dynamics and reactivity of biomolecular systems using molecular modelling tools.
- Syllabus
- Basic requirements for models of biomolecular systems * Limitation of experimental (X-ray, NMR, CryoEM) and predicted (AlphaFold2, ESM-Fold, RoseTTAFold2) structures * Ionizable groups and the effect of pH on the model * Docking of substrates into the active site * How to solvate biomolecular systems correctly * Types of water and ion models * Molecular dynamics (MD) of biomolecular systems * Analysis of MD trajectories * Hybrid QM/MM description of the active site of an enzymatic reaction * Calculation of reaction profiles * Study of reaction mechanisms
- Literature
- Encyclopedia of computational chemistry. Edited by Paul von R. Schleyer. Chichester: John Wiley & sons, 1998, xxix, 812. ISBN 047196588X. info
- LEACH, Andrew R. Molecular modelling : principles and applications. 2nd ed. Harlow: Prentice Hall, 2001, xxiii, 744. ISBN 0582382106. info
- JENSEN, Frank. Introduction to computational chemistry. Third edition. Chichester: Wiley, 2017, xxii, 638. ISBN 9781118825990. info
- Teaching methods
- Lectures combined with discussions.
- Assessment methods
- The course ends with a written test followed by an optional oral examination.
- Language of instruction
- Czech
- Further Comments
- The course can also be completed outside the examination period.
The course is taught annually.
The course is taught: every week.
C8855 Advanced Molecular Modelling Methods
Faculty of ScienceSpring 2023
- Extent and Intensity
- 1/0/0. 1 credit(s) (plus extra credits for completion). Recommended Type of Completion: k (colloquium). Other types of completion: zk (examination).
- Teacher(s)
- RNDr. Petr Kulhánek, Ph.D. (lecturer)
Mgr. Ivo Durník, Ph.D. (seminar tutor) - Guaranteed by
- RNDr. Petr Kulhánek, Ph.D.
National Centre for Biomolecular Research – Faculty of Science
Contact Person: RNDr. Petr Kulhánek, Ph.D.
Supplier department: National Centre for Biomolecular Research – Faculty of Science - Timetable
- Wed 9:00–9:50 C04/118
- Prerequisites
- Basic level of general and physical chemistry. A basic knowledge in quantum chemistry is an advantage. It is strongly suggested that the student went through the course C7790/C7800. It is likely that the course is mainly for PhD students.
- Course Enrolment Limitations
- The course is also offered to the students of the fields other than those the course is directly associated with.
- fields of study / plans the course is directly associated with
- Macromolecular Chemistry (programme PřF, D-CH) (2)
- Organic Chemistry (programme PřF, N-CH)
- Course objectives
- At the end of the course students should have basic knowledge in the field of computational chemistry. Basic knowledge about methods to analyze complicated energy functions will be gained together with knowledge about molecular dynamics simulations and studies on molecular complexes and chemical reactions. Also methods how to include solvent are discussed. Practical part of the course is oriented to work with an existing program package.
- Learning outcomes
- Student will have basic knowledge in the field of computational chemistry including knowledge about methods to analyze complicated energy functions and knowledge about molecular dynamics simulations, molecular complexes and chemical reactions. Student will be able to include solvent in the calculations. Students will be able to work with a selected program package.
- Syllabus
- 1. Potential Energy Hypersurfaces. Stationary points and basic algorithms to search for them. 2. Simulation methods - molecular dynamics and Monte Carlo. 3. Conformational analysis in computational chemistry. 4. Computational chemistry of supramolecules, molecular complexes and biomolecules. Docking. Designing of new molecules. 5. Solvent modeling. 6. Chemical reactions modeling. 7. Program systems Insight II, AMBER, DISCOVER, Oxford Molecular, WHATIF, AUTODOCK.
- Literature
- Lipkowitz, K B - Boyd, D B. Reviews in Computational Chemistry 1-9. New York : VCH Publishers, 1998.
- JENSEN, Frank. Introduction to Computational Chemistry. New York: J. Wiley & Sons Ltd., 1999. info
- HEHRE, Warren J., Alan J. SHUSTERMAN and W. Wayne HUANG. A laboratory book of computational organic chemistry. Irvine, Calif.: Wavefunction, 1996, xiv, 291 s. ISBN 0-9643495-5-8. info
- FORESMAN, J B and A FRISCH. Exploring Chemistry with Electronic Structure Methods. Pittsburgh: Gaussian, Inc., 1996. info
- Teaching methods
- Lectures combined with discussions.
- Assessment methods
- Oral examination
- Language of instruction
- Czech
- Further Comments
- Study Materials
The course can also be completed outside the examination period.
The course is taught annually.
C8855 Advanced Molecular Modelling Methods
Faculty of ScienceSpring 2022
- Extent and Intensity
- 1/0/0. 1 credit(s) (plus extra credits for completion). Recommended Type of Completion: k (colloquium). Other types of completion: zk (examination).
- Teacher(s)
- RNDr. Petr Kulhánek, Ph.D. (lecturer)
Mgr. Ivo Durník, Ph.D. (seminar tutor) - Guaranteed by
- RNDr. Petr Kulhánek, Ph.D.
National Centre for Biomolecular Research – Faculty of Science
Contact Person: RNDr. Petr Kulhánek, Ph.D.
Supplier department: National Centre for Biomolecular Research – Faculty of Science - Timetable
- Wed 9:00–9:50 C04/118
- Prerequisites
- Basic level of general and physical chemistry. A basic knowledge in quantum chemistry is an advantage. It is strongly suggested that the student went through the course C7790/C7800. It is likely that the course is mainly for PhD students.
- Course Enrolment Limitations
- The course is also offered to the students of the fields other than those the course is directly associated with.
- fields of study / plans the course is directly associated with
- Macromolecular Chemistry (programme PřF, D-CH) (2)
- Organic Chemistry (programme PřF, N-CH)
- Course objectives
- At the end of the course students should have basic knowledge in the field of computational chemistry. Basic knowledge about methods to analyze complicated energy functions will be gained together with knowledge about molecular dynamics simulations and studies on molecular complexes and chemical reactions. Also methods how to include solvent are discussed. Practical part of the course is oriented to work with an existing program package.
- Learning outcomes
- Student will have basic knowledge in the field of computational chemistry including knowledge about methods to analyze complicated energy functions and knowledge about molecular dynamics simulations, molecular complexes and chemical reactions. Student will be able to include solvent in the calculations. Students will be able to work with a selected program package.
- Syllabus
- 1. Potential Energy Hypersurfaces. Stationary points and basic algorithms to search for them. 2. Simulation methods - molecular dynamics and Monte Carlo. 3. Conformational analysis in computational chemistry. 4. Computational chemistry of supramolecules, molecular complexes and biomolecules. Docking. Designing of new molecules. 5. Solvent modeling. 6. Chemical reactions modeling. 7. Program systems Insight II, AMBER, DISCOVER, Oxford Molecular, WHATIF, AUTODOCK.
- Literature
- Lipkowitz, K B - Boyd, D B. Reviews in Computational Chemistry 1-9. New York : VCH Publishers, 1998.
- JENSEN, Frank. Introduction to Computational Chemistry. New York: J. Wiley & Sons Ltd., 1999. info
- HEHRE, Warren J., Alan J. SHUSTERMAN and W. Wayne HUANG. A laboratory book of computational organic chemistry. Irvine, Calif.: Wavefunction, 1996, xiv, 291 s. ISBN 0-9643495-5-8. info
- FORESMAN, J B and A FRISCH. Exploring Chemistry with Electronic Structure Methods. Pittsburgh: Gaussian, Inc., 1996. info
- Teaching methods
- Lectures combined with discussions.
- Assessment methods
- Oral examination
- Language of instruction
- Czech
- Further Comments
- Study Materials
The course can also be completed outside the examination period.
The course is taught annually.
C8855 Computational Chemistry and Molecular Modeling II
Faculty of ScienceSpring 2021
- Extent and Intensity
- 1/0/0. 1 credit(s) (plus extra credits for completion). Recommended Type of Completion: k (colloquium). Other types of completion: zk (examination).
- Teacher(s)
- prof. RNDr. Jaroslav Koča, DrSc. (lecturer)
RNDr. Petr Kulhánek, Ph.D. (lecturer) - Guaranteed by
- RNDr. Petr Kulhánek, Ph.D.
National Centre for Biomolecular Research – Faculty of Science
Contact Person: prof. RNDr. Jaroslav Koča, DrSc.
Supplier department: National Centre for Biomolecular Research – Faculty of Science - Timetable
- Mon 1. 3. to Fri 14. 5. Thu 10:00–10:50 C04/118
- Prerequisites
- Basic level of general and physical chemistry. A basic knowledge in quantum chemistry is an advantage. It is strongly suggested that the student went through the course C7790/C7800. It is likely that the course is mainly for PhD students.
- Course Enrolment Limitations
- The course is also offered to the students of the fields other than those the course is directly associated with.
- fields of study / plans the course is directly associated with
- Macromolecular Chemistry (programme PřF, D-CH) (2)
- Organic Chemistry (programme PřF, N-CH)
- Course objectives
- At the end of the course students should have basic knowledge in the field of computational chemistry. Basic knowledge about methods to analyze complicated energy functions will be gained together with knowledge about molecular dynamics simulations and studies on molecular complexes and chemical reactions. Also methods how to include solvent are discussed. Practical part of the course is oriented to work with an existing program package.
- Learning outcomes
- Student will have basic knowledge in the field of computational chemistry including knowledge about methods to analyze complicated energy functions and knowledge about molecular dynamics simulations, molecular complexes and chemical reactions. Student will be able to include solvent in the calculations. Students will be able to work with a selected program package.
- Syllabus
- 1. Potential Energy Hypersurfaces. Stationary points and basic algorithms to search for them. 2. Simulation methods - molecular dynamics and Monte Carlo. 3. Conformational analysis in computational chemistry. 4. Computational chemistry of supramolecules, molecular complexes and biomolecules. Docking. Designing of new molecules. 5. Solvent modeling. 6. Chemical reactions modeling. 7. Program systems Insight II, AMBER, DISCOVER, Oxford Molecular, WHATIF, AUTODOCK.
- Literature
- Lipkowitz, K B - Boyd, D B. Reviews in Computational Chemistry 1-9. New York : VCH Publishers, 1998.
- JENSEN, Frank. Introduction to Computational Chemistry. New York: J. Wiley & Sons Ltd., 1999. info
- HEHRE, Warren J., Alan J. SHUSTERMAN and W. Wayne HUANG. A laboratory book of computational organic chemistry. Irvine, Calif.: Wavefunction, 1996, xiv, 291 s. ISBN 0-9643495-5-8. info
- FORESMAN, J B and A FRISCH. Exploring Chemistry with Electronic Structure Methods. Pittsburgh: Gaussian, Inc., 1996. info
- Teaching methods
- Lectures combined with discussions.
- Assessment methods
- Oral examination
- Language of instruction
- Czech
- Further Comments
- Study Materials
The course can also be completed outside the examination period.
The course is taught annually.
C8855 Computational Chemistry and Molecular Modeling II
Faculty of ScienceSpring 2020
- Extent and Intensity
- 1/0/0. 1 credit(s) (plus extra credits for completion). Recommended Type of Completion: k (colloquium). Other types of completion: zk (examination).
- Teacher(s)
- prof. RNDr. Jaroslav Koča, DrSc. (lecturer)
RNDr. Petr Kulhánek, Ph.D. (lecturer) - Guaranteed by
- RNDr. Petr Kulhánek, Ph.D.
National Centre for Biomolecular Research – Faculty of Science
Contact Person: prof. RNDr. Jaroslav Koča, DrSc.
Supplier department: National Centre for Biomolecular Research – Faculty of Science - Timetable
- Wed 9:00–9:50 C04/118
- Prerequisites
- Basic level of general and physical chemistry. A basic knowledge in quantum chemistry is an advantage. It is strongly suggested that the student went through the course C7790/C7800. It is likely that the course is mainly for PhD students.
- Course Enrolment Limitations
- The course is also offered to the students of the fields other than those the course is directly associated with.
- fields of study / plans the course is directly associated with
- Macromolecular Chemistry (programme PřF, D-CH) (2)
- Organic Chemistry (programme PřF, N-CH)
- Course objectives
- At the end of the course students should have basic knowledge in the field of computational chemistry. Basic knowledge about methods to analyze complicated energy functions will be gained together with knowledge about molecular dynamics simulations and studies on molecular complexes and chemical reactions. Also methods how to include solvent are discussed. Practical part of the course is oriented to work with an existing program package.
- Learning outcomes
- Student will have basic knowledge in the field of computational chemistry including knowledge about methods to analyze complicated energy functions and knowledge about molecular dynamics simulations, molecular complexes and chemical reactions. Student will be able to include solvent in the calculations. Students will be able to work with a selected program package.
- Syllabus
- 1. Potential Energy Hypersurfaces. Stationary points and basic algorithms to search for them. 2. Simulation methods - molecular dynamics and Monte Carlo. 3. Conformational analysis in computational chemistry. 4. Computational chemistry of supramolecules, molecular complexes and biomolecules. Docking. Designing of new molecules. 5. Solvent modeling. 6. Chemical reactions modeling. 7. Program systems Insight II, AMBER, DISCOVER, Oxford Molecular, WHATIF, AUTODOCK.
- Literature
- Lipkowitz, K B - Boyd, D B. Reviews in Computational Chemistry 1-9. New York : VCH Publishers, 1998.
- JENSEN, Frank. Introduction to Computational Chemistry. New York: J. Wiley & Sons Ltd., 1999. info
- HEHRE, Warren J., Alan J. SHUSTERMAN and W. Wayne HUANG. A laboratory book of computational organic chemistry. Irvine, Calif.: Wavefunction, 1996, xiv, 291 s. ISBN 0-9643495-5-8. info
- FORESMAN, J B and A FRISCH. Exploring Chemistry with Electronic Structure Methods. Pittsburgh: Gaussian, Inc., 1996. info
- Teaching methods
- Lectures combined with discussions.
- Assessment methods
- Oral examination
- Language of instruction
- Czech
- Further Comments
- Study Materials
The course can also be completed outside the examination period.
The course is taught annually.
C8855 Computational Chemistry and Molecular Modeling II
Faculty of ScienceSpring 2019
- Extent and Intensity
- 1/0/0. 1 credit(s) (plus extra credits for completion). Recommended Type of Completion: k (colloquium). Other types of completion: zk (examination).
- Teacher(s)
- prof. RNDr. Jaroslav Koča, DrSc. (lecturer)
Mgr. Zdeněk Kříž, Ph.D. (lecturer) - Guaranteed by
- prof. RNDr. Jaroslav Koča, DrSc.
National Centre for Biomolecular Research – Faculty of Science
Contact Person: prof. RNDr. Jaroslav Koča, DrSc.
Supplier department: National Centre for Biomolecular Research – Faculty of Science - Prerequisites
- Basic level of general and physical chemistry. A basic knowledge in quantum chemistry is an advantage. It is strongly suggested that the student went through the course C7790/C7800. It is likely that the course is mainly for PhD students.
- Course Enrolment Limitations
- The course is also offered to the students of the fields other than those the course is directly associated with.
- fields of study / plans the course is directly associated with
- Macromolecular Chemistry (programme PřF, D-CH) (2)
- Organic Chemistry (programme PřF, N-CH)
- Course objectives
- At the end of the course students should have basic knowledge in the field of computational chemistry. Basic knowledge about methods to analyze complicated energy functions will be gained together with knowledge about molecular dynamics simulations and studies on molecular complexes and chemical reactions. Also methods how to include solvent are discussed. Practical part of the course is oriented to work with an existing program package.
- Syllabus
- 1. Potential Energy Hypersurfaces. Stationary points and basic algorithms to search for them. 2. Simulation methods - molecular dynamics and Monte Carlo. 3. Conformational analysis in computational chemistry. 4. Computational chemistry of supramolecules, molecular complexes and biomolecules. Docking. Designing of new molecules. 5. Solvent modeling. 6. Chemical reactions modeling. 7. Program systems Insight II, AMBER, DISCOVER, Oxford Molecular, WHATIF, AUTODOCK.
- Literature
- Lipkowitz, K B - Boyd, D B. Reviews in Computational Chemistry 1-9. New York : VCH Publishers, 1998.
- JENSEN, Frank. Introduction to Computational Chemistry. New York: J. Wiley & Sons Ltd., 1999. info
- HEHRE, Warren J., Alan J. SHUSTERMAN and W. Wayne HUANG. A laboratory book of computational organic chemistry. Irvine, Calif.: Wavefunction, 1996, xiv, 291 s. ISBN 0-9643495-5-8. info
- FORESMAN, J B and A FRISCH. Exploring Chemistry with Electronic Structure Methods. Pittsburgh: Gaussian, Inc., 1996. info
- Teaching methods
- Lectures combined with discussions.
- Assessment methods
- Oral examination
- Language of instruction
- Czech
- Further Comments
- The course can also be completed outside the examination period.
The course is taught annually.
The course is taught: every week.
C8855 Computational Chemistry and Molecular Modeling II
Faculty of Sciencespring 2018
- Extent and Intensity
- 1/0/0. 1 credit(s) (plus extra credits for completion). Recommended Type of Completion: k (colloquium). Other types of completion: zk (examination).
- Teacher(s)
- prof. RNDr. Jaroslav Koča, DrSc. (lecturer)
Mgr. Zdeněk Kříž, Ph.D. (lecturer) - Guaranteed by
- prof. RNDr. Jaroslav Koča, DrSc.
National Centre for Biomolecular Research – Faculty of Science
Contact Person: prof. RNDr. Jaroslav Koča, DrSc.
Supplier department: National Centre for Biomolecular Research – Faculty of Science - Prerequisites
- Basic level of general and physical chemistry. A basic knowledge in quantum chemistry is an advantage. It is strongly suggested that the student went through the course C7790/C7800. It is likely that the course is mainly for PhD students.
- Course Enrolment Limitations
- The course is also offered to the students of the fields other than those the course is directly associated with.
- fields of study / plans the course is directly associated with
- Macromolecular Chemistry (programme PřF, D-CH) (2)
- Organic Chemistry (programme PřF, N-CH)
- Course objectives
- At the end of the course students should have basic knowledge in the field of computational chemistry. Basic knowledge about methods to analyze complicated energy functions will be gained together with knowledge about molecular dynamics simulations and studies on molecular complexes and chemical reactions. Also methods how to include solvent are discussed. Practical part of the course is oriented to work with an existing program package.
- Syllabus
- 1. Potential Energy Hypersurfaces. Stationary points and basic algorithms to search for them. 2. Simulation methods - molecular dynamics and Monte Carlo. 3. Conformational analysis in computational chemistry. 4. Computational chemistry of supramolecules, molecular complexes and biomolecules. Docking. Designing of new molecules. 5. Solvent modeling. 6. Chemical reactions modeling. 7. Program systems Insight II, AMBER, DISCOVER, Oxford Molecular, WHATIF, AUTODOCK.
- Literature
- Lipkowitz, K B - Boyd, D B. Reviews in Computational Chemistry 1-9. New York : VCH Publishers, 1998.
- JENSEN, Frank. Introduction to Computational Chemistry. New York: J. Wiley & Sons Ltd., 1999. info
- HEHRE, Warren J., Alan J. SHUSTERMAN and W. Wayne HUANG. A laboratory book of computational organic chemistry. Irvine, Calif.: Wavefunction, 1996, xiv, 291 s. ISBN 0-9643495-5-8. info
- FORESMAN, J B and A FRISCH. Exploring Chemistry with Electronic Structure Methods. Pittsburgh: Gaussian, Inc., 1996. info
- Teaching methods
- Lectures combined with discussions.
- Assessment methods
- Oral examination
- Language of instruction
- Czech
- Further Comments
- Study Materials
The course can also be completed outside the examination period.
The course is taught annually.
The course is taught: every week.
C8855 Computational Chemistry and Molecular Modeling II
Faculty of ScienceSpring 2017
- Extent and Intensity
- 1/0/0. 1 credit(s) (plus extra credits for completion). Recommended Type of Completion: k (colloquium). Other types of completion: zk (examination).
- Teacher(s)
- prof. RNDr. Jaroslav Koča, DrSc. (lecturer)
Mgr. Zdeněk Kříž, Ph.D. (lecturer) - Guaranteed by
- prof. RNDr. Jaroslav Koča, DrSc.
National Centre for Biomolecular Research – Faculty of Science
Contact Person: prof. RNDr. Jaroslav Koča, DrSc.
Supplier department: National Centre for Biomolecular Research – Faculty of Science - Prerequisites
- Basic level of general and physical chemistry. A basic knowledge in quantum chemistry is an advantage. It is strongly suggested that the student went through the course C7790/C7800. It is likely that the course is mainly for PhD students.
- Course Enrolment Limitations
- The course is also offered to the students of the fields other than those the course is directly associated with.
- fields of study / plans the course is directly associated with
- Macromolecular Chemistry (programme PřF, D-CH) (2)
- Organic Chemistry (programme PřF, N-CH)
- Course objectives
- At the end of the course students should have basic knowledge in the field of computational chemistry. Basic knowledge about methods to analyze complicated energy functions will be gained together with knowledge about molecular dynamics simulations and studies on molecular complexes and chemical reactions. Also methods how to include solvent are discussed. Practical part of the course is oriented to work with an existing program package.
- Syllabus
- 1. Potential Energy Hypersurfaces. Stationary points and basic algorithms to search for them. 2. Simulation methods - molecular dynamics and Monte Carlo. 3. Conformational analysis in computational chemistry. 4. Computational chemistry of supramolecules, molecular complexes and biomolecules. Docking. Designing of new molecules. 5. Solvent modeling. 6. Chemical reactions modeling. 7. Program systems Insight II, AMBER, DISCOVER, Oxford Molecular, WHATIF, AUTODOCK.
- Literature
- Lipkowitz, K B - Boyd, D B. Reviews in Computational Chemistry 1-9. New York : VCH Publishers, 1998.
- JENSEN, Frank. Introduction to Computational Chemistry. New York: J. Wiley & Sons Ltd., 1999. info
- HEHRE, Warren J., Alan J. SHUSTERMAN and W. Wayne HUANG. A laboratory book of computational organic chemistry. Irvine, Calif.: Wavefunction, 1996, xiv, 291 s. ISBN 0-9643495-5-8. info
- FORESMAN, J B and A FRISCH. Exploring Chemistry with Electronic Structure Methods. Pittsburgh: Gaussian, Inc., 1996. info
- Teaching methods
- Lectures combined with discussions.
- Assessment methods
- Oral examination
- Language of instruction
- Czech
- Further Comments
- The course can also be completed outside the examination period.
The course is taught annually.
The course is taught: every week.
C8855 Computational Chemistry and Molecular Modeling II
Faculty of ScienceSpring 2016
- Extent and Intensity
- 1/0/0. 1 credit(s) (plus extra credits for completion). Recommended Type of Completion: k (colloquium). Other types of completion: zk (examination).
- Teacher(s)
- prof. RNDr. Jaroslav Koča, DrSc. (lecturer)
Mgr. Zdeněk Kříž, Ph.D. (lecturer) - Guaranteed by
- prof. RNDr. Jaroslav Koča, DrSc.
National Centre for Biomolecular Research – Faculty of Science
Contact Person: prof. RNDr. Jaroslav Koča, DrSc.
Supplier department: National Centre for Biomolecular Research – Faculty of Science - Timetable
- Fri 10:00–10:50 C04/118
- Prerequisites
- Basic level of general and physical chemistry. A basic knowledge in quantum chemistry is an advantage. It is strongly suggested that the student went through the course C7790/C7800. It is likely that the course is mainly for PhD students.
- Course Enrolment Limitations
- The course is also offered to the students of the fields other than those the course is directly associated with.
- fields of study / plans the course is directly associated with
- Macromolecular Chemistry (programme PřF, D-CH) (2)
- Organic Chemistry (programme PřF, N-CH)
- Course objectives
- At the end of the course students should have basic knowledge in the field of computational chemistry. Basic knowledge about methods to analyze complicated energy functions will be gained together with knowledge about molecular dynamics simulations and studies on molecular complexes and chemical reactions. Also methods how to include solvent are discussed. Practical part of the course is oriented to work with an existing program package.
- Syllabus
- 1. Potential Energy Hypersurfaces. Stationary points and basic algorithms to search for them. 2. Simulation methods - molecular dynamics and Monte Carlo. 3. Conformational analysis in computational chemistry. 4. Computational chemistry of supramolecules, molecular complexes and biomolecules. Docking. Designing of new molecules. 5. Solvent modeling. 6. Chemical reactions modeling. 7. Program systems Insight II, AMBER, DISCOVER, Oxford Molecular, WHATIF, AUTODOCK.
- Literature
- Lipkowitz, K B - Boyd, D B. Reviews in Computational Chemistry 1-9. New York : VCH Publishers, 1998.
- JENSEN, Frank. Introduction to Computational Chemistry. New York: J. Wiley & Sons Ltd., 1999. info
- HEHRE, Warren J., Alan J. SHUSTERMAN and W. Wayne HUANG. A laboratory book of computational organic chemistry. Irvine, Calif.: Wavefunction, 1996, xiv, 291 s. ISBN 0-9643495-5-8. info
- FORESMAN, J B and A FRISCH. Exploring Chemistry with Electronic Structure Methods. Pittsburgh: Gaussian, Inc., 1996. info
- Teaching methods
- Lectures combined with discussions.
- Assessment methods
- Oral examination
- Language of instruction
- Czech
- Further Comments
- The course can also be completed outside the examination period.
The course is taught annually.
C8855 Computational Chemistry and Molecular Modeling II
Faculty of ScienceSpring 2015
- Extent and Intensity
- 1/0/0. 1 credit(s) (plus extra credits for completion). Recommended Type of Completion: k (colloquium). Other types of completion: zk (examination).
- Teacher(s)
- prof. RNDr. Jaroslav Koča, DrSc. (lecturer)
Mgr. Zdeněk Kříž, Ph.D. (lecturer) - Guaranteed by
- prof. RNDr. Jaroslav Koča, DrSc.
National Centre for Biomolecular Research – Faculty of Science
Contact Person: prof. RNDr. Jaroslav Koča, DrSc.
Supplier department: National Centre for Biomolecular Research – Faculty of Science - Timetable
- Fri 10:00–10:50 C04/118
- Prerequisites
- Basic level of general and physical chemistry. A basic knowledge in quantum chemistry is an advantage. It is strongly suggested that the student went through the course C7790/C7800. It is likely that the course is mainly for PhD students.
- Course Enrolment Limitations
- The course is also offered to the students of the fields other than those the course is directly associated with.
- fields of study / plans the course is directly associated with
- Macromolecular Chemistry (programme PřF, D-CH) (2)
- Organic Chemistry (programme PřF, N-CH)
- Course objectives
- At the end of the course students should have basic knowledge in the field of computational chemistry. Basic knowledge about methods to analyze complicated energy functions will be gained together with knowledge about molecular dynamics simulations and studies on molecular complexes and chemical reactions. Also methods how to include solvent are discussed. Practical part of the course is oriented to work with an existing program package.
- Syllabus
- 1. Potential Energy Hypersurfaces. Stationary points and basic algorithms to search for them. 2. Simulation methods - molecular dynamics and Monte Carlo. 3. Conformational analysis in computational chemistry. 4. Computational chemistry of supramolecules, molecular complexes and biomolecules. Docking. Designing of new molecules. 5. Solvent modeling. 6. Chemical reactions modeling. 7. Program systems Insight II, AMBER, DISCOVER, Oxford Molecular, WHATIF, AUTODOCK.
- Literature
- Lipkowitz, K B - Boyd, D B. Reviews in Computational Chemistry 1-9. New York : VCH Publishers, 1998.
- JENSEN, Frank. Introduction to Computational Chemistry. New York: J. Wiley & Sons Ltd., 1999. info
- HEHRE, Warren J., Alan J. SHUSTERMAN and W. Wayne HUANG. A laboratory book of computational organic chemistry. Irvine, Calif.: Wavefunction, 1996, xiv, 291 s. ISBN 0-9643495-5-8. info
- FORESMAN, J B and A FRISCH. Exploring Chemistry with Electronic Structure Methods. Pittsburgh: Gaussian, Inc., 1996. info
- Teaching methods
- Lectures combined with discussions.
- Assessment methods
- Oral examination
- Language of instruction
- Czech
- Further Comments
- Study Materials
The course can also be completed outside the examination period.
The course is taught annually.
C8855 Computational Chemistry and Molecular Modeling II
Faculty of ScienceSpring 2014
- Extent and Intensity
- 1/0/0. 1 credit(s) (plus extra credits for completion). Recommended Type of Completion: k (colloquium). Other types of completion: zk (examination).
- Teacher(s)
- prof. RNDr. Jaroslav Koča, DrSc. (lecturer)
Mgr. Zdeněk Kříž, Ph.D. (lecturer) - Guaranteed by
- prof. RNDr. Jaroslav Koča, DrSc.
National Centre for Biomolecular Research – Faculty of Science
Contact Person: prof. RNDr. Jaroslav Koča, DrSc.
Supplier department: National Centre for Biomolecular Research – Faculty of Science - Timetable
- Fri 10:00–10:50 C04/118
- Prerequisites
- Basic level of general and physical chemistry. A basic knowledge in quantum chemistry is an advantage. It is strongly suggested that the student went through the course C7790/C7800. It is likely that the course is mainly for PhD students.
- Course Enrolment Limitations
- The course is also offered to the students of the fields other than those the course is directly associated with.
- fields of study / plans the course is directly associated with
- Macromolecular Chemistry (programme PřF, D-CH) (2)
- Organic Chemistry (programme PřF, N-CH)
- Course objectives
- At the end of the course students should have basic knowledge in the field of computational chemistry. Basic knowledge about methods to analyze complicated energy functions will be gained together with knowledge about molecular dynamics simulations and studies on molecular complexes and chemical reactions. Also methods how to include solvent are discussed. Practical part of the course is oriented to work with an existing program package.
- Syllabus
- 1. Potential Energy Hypersurfaces. Stationary points and basic algorithms to search for them. 2. Simulation methods - molecular dynamics and Monte Carlo. 3. Conformational analysis in computational chemistry. 4. Computational chemistry of supramolecules, molecular complexes and biomolecules. Docking. Designing of new molecules. 5. Solvent modeling. 6. Chemical reactions modeling. 7. Program systems Insight II, AMBER, DISCOVER, Oxford Molecular, WHATIF, AUTODOCK.
- Literature
- Lipkowitz, K B - Boyd, D B. Reviews in Computational Chemistry 1-9. New York : VCH Publishers, 1998.
- JENSEN, Frank. Introduction to Computational Chemistry. New York: J. Wiley & Sons Ltd., 1999. info
- HEHRE, Warren J., Alan J. SHUSTERMAN and W. Wayne HUANG. A laboratory book of computational organic chemistry. Irvine, Calif.: Wavefunction, 1996, xiv, 291 s. ISBN 0-9643495-5-8. info
- FORESMAN, J B and A FRISCH. Exploring Chemistry with Electronic Structure Methods. Pittsburgh: Gaussian, Inc., 1996. info
- Teaching methods
- Lectures combined with discussions.
- Assessment methods
- Oral examination
- Language of instruction
- Czech
- Further Comments
- Study Materials
The course can also be completed outside the examination period.
The course is taught annually.
C8855 Computational Chemistry and Molecular Modeling II
Faculty of ScienceSpring 2013
- Extent and Intensity
- 1/0/0. 1 credit(s) (plus extra credits for completion). Recommended Type of Completion: k (colloquium). Other types of completion: zk (examination).
- Teacher(s)
- prof. RNDr. Jaroslav Koča, DrSc. (lecturer)
Mgr. Zdeněk Kříž, Ph.D. (lecturer) - Guaranteed by
- prof. RNDr. Jaroslav Koča, DrSc.
National Centre for Biomolecular Research – Faculty of Science
Contact Person: prof. RNDr. Jaroslav Koča, DrSc.
Supplier department: National Centre for Biomolecular Research – Faculty of Science - Timetable
- Fri 10:00–10:50 C04/118
- Prerequisites
- Basic level of general and physical chemistry. A basic knowledge in quantum chemistry is an advantage. It is strongly suggested that the student went through the course C7790/C7800. It is likely that the course is mainly for PhD students.
- Course Enrolment Limitations
- The course is also offered to the students of the fields other than those the course is directly associated with.
- fields of study / plans the course is directly associated with
- Macromolecular Chemistry (programme PřF, D-CH) (2)
- Organic Chemistry (programme PřF, N-CH)
- Course objectives
- At the end of the course students should have basic knowledge in the field of computational chemistry. Basic knowledge about methods to analyze complicated energy functions will be gained together with knowledge about molecular dynamics simulations and studies on molecular complexes and chemical reactions. Also methods how to include solvent are discussed. Practical part of the course is oriented to work with an existing program package.
- Syllabus
- 1. Potential Energy Hypersurfaces. Stationary points and basic algorithms to search for them. 2. Simulation methods - molecular dynamics and Monte Carlo. 3. Conformational analysis in computational chemistry. 4. Computational chemistry of supramoleculas, molecular complexes and biomolecules. Docking. Designing of new molecules. 5. Solvent modeling. 6. Chemical reactions modeling. 7. Program systems Insight II, AMBER, DISCOVER, Oxford Molecular, WHATIF, AUTODOCK.
- Literature
- Lipkowitz, K B - Boyd, D B. Reviews in Computational Chemistry 1-9. New York : VCH Publishers, 1998.
- JENSEN, Frank. Introduction to Computational Chemistry. New York: J. Wiley & Sons Ltd., 1999. info
- HEHRE, Warren J., Alan J. SHUSTERMAN and W. Wayne HUANG. A laboratory book of computational organic chemistry. Irvine, Calif.: Wavefunction, 1996, xiv, 291 s. ISBN 0-9643495-5-8. info
- FORESMAN, J B and A FRISCH. Exploring Chemistry with Electronic Structure Methods. Pittsburgh: Gaussian, Inc., 1996. info
- Teaching methods
- Lectures combined with discussions.
- Assessment methods
- Oral examination
- Language of instruction
- Czech
- Further Comments
- Study Materials
The course can also be completed outside the examination period.
The course is taught annually.
C8855 Computational Chemistry and Molecular Modeling II
Faculty of ScienceSpring 2012
- Extent and Intensity
- 1/0/0. 1 credit(s) (plus extra credits for completion). Recommended Type of Completion: k (colloquium). Other types of completion: zk (examination).
- Teacher(s)
- prof. RNDr. Jaroslav Koča, DrSc. (lecturer)
Mgr. Zdeněk Kříž, Ph.D. (lecturer) - Guaranteed by
- prof. RNDr. Jaroslav Koča, DrSc.
National Centre for Biomolecular Research – Faculty of Science
Contact Person: prof. RNDr. Jaroslav Koča, DrSc.
Supplier department: National Centre for Biomolecular Research – Faculty of Science - Timetable
- Fri 10:00–10:50 C04/118
- Prerequisites
- Basic level of general and physical chemistry. A basic knowledge in quantum chemistry is an advantage. It is strongly suggested that the student went through the course C7790/C7800. It is likely that the course is mainly for PhD students.
- Course Enrolment Limitations
- The course is also offered to the students of the fields other than those the course is directly associated with.
- fields of study / plans the course is directly associated with
- Macromolecular Chemistry (programme PřF, D-CH) (2)
- Organic Chemistry (programme PřF, N-CH)
- Course objectives
- At the end of the course students should have basic knowledge in the field of computational chemistry. Basic knowledge about methods to analyze complicated energy functions will be gained together with knowledge about molecular dynamics simulations and studies on molecular complexes and chemical reactions. Also methods how to include solvent are discussed. Practical part of the course is oriented to work with an existing program package.
- Syllabus
- 1. Potential Energy Hypersurfaces. Stationary points and basic algorithms to search for them. 2. Simulation methods - molecular dynamics and Monte Carlo. 3. Conformational analysis in computational chemistry. 4. Computational chemistry of supramoleculas, molecular complexes and biomolecules. Docking. Designing of new molecules. 5. Solvent modeling. 6. Chemical reactions modeling. 7. Program systems Insight II, AMBER, DISCOVER, Oxford Molecular, WHATIF, AUTODOCK.
- Literature
- Lipkowitz, K B - Boyd, D B. Reviews in Computational Chemistry 1-9. New York : VCH Publishers, 1998.
- JENSEN, Frank. Introduction to Computational Chemistry. New York: J. Wiley & Sons Ltd., 1999. info
- HEHRE, Warren J., Alan J. SHUSTERMAN and W. Wayne HUANG. A laboratory book of computational organic chemistry. Irvine, Calif.: Wavefunction, 1996, xiv, 291 s. ISBN 0-9643495-5-8. info
- FORESMAN, J B and A FRISCH. Exploring Chemistry with Electronic Structure Methods. Pittsburgh: Gaussian, Inc., 1996. info
- Teaching methods
- Lectures combined with discussions.
- Assessment methods
- Oral examination
- Language of instruction
- Czech
- Further Comments
- Study Materials
The course can also be completed outside the examination period.
The course is taught annually.
C8855 Computational Chemistry and Molecular Modeling II
Faculty of ScienceSpring 2011
- Extent and Intensity
- 1/0/0. 2 credit(s). Recommended Type of Completion: k (colloquium). Other types of completion: zk (examination).
- Teacher(s)
- prof. RNDr. Jaroslav Koča, DrSc. (lecturer)
Mgr. Zdeněk Kříž, Ph.D. (lecturer) - Guaranteed by
- prof. RNDr. Jaroslav Koča, DrSc.
National Centre for Biomolecular Research – Faculty of Science
Contact Person: prof. RNDr. Jaroslav Koča, DrSc. - Timetable
- Thu 9:00–9:50 C04/211
- Prerequisites
- Basic level of general and physical chemistry. A basic knowledge in quantum chemistry is an advantage. It is strongly suggested that the student went through the course C7790/C7800. It is likely that the course is mainly for PhD students.
- Course Enrolment Limitations
- The course is also offered to the students of the fields other than those the course is directly associated with.
- fields of study / plans the course is directly associated with
- there are 21 fields of study the course is directly associated with, display
- Course objectives
- At the end of the course students should have basic knowledge in the field of computational chemistry. Basic knowledge about methods to analyze complicated energy functions will be gained together with knowledge about molecular dynamics simulations and studies on molecular complexes and chemical reactions. Also methods how to include solvent are discussed. Practical part of the course is oriented to work with an existing program package.
- Syllabus
- 1. Potential Energy Hypersurfaces. Stationary points and basic algorithms to search for them. 2. Simulation methods - molecular dynamics and Monte Carlo. 3. Conformational analysis in computational chemistry. 4. Computational chemistry of supramoleculas, molecular complexes and biomolecules. Docking. Designing of new molecules. 5. Solvent modeling. 6. Chemical reactions modeling. 7. Program systems Insight II, AMBER, DISCOVER, Oxford Molecular, WHATIF, AUTODOCK.
- Literature
- Lipkowitz, K B - Boyd, D B. Reviews in Computational Chemistry 1-9. New York : VCH Publishers, 1998.
- JENSEN, Frank. Introduction to Computational Chemistry. New York: J. Wiley & Sons Ltd., 1999. info
- HEHRE, Warren J., Alan J. SHUSTERMAN and W. Wayne HUANG. A laboratory book of computational organic chemistry. Irvine, Calif.: Wavefunction, 1996, xiv, 291 s. ISBN 0-9643495-5-8. info
- FORESMAN, J B and A FRISCH. Exploring Chemistry with Electronic Structure Methods. Pittsburgh: Gaussian, Inc., 1996. info
- Teaching methods
- Lectures combined with discussions.
- Assessment methods
- Oral examination
- Language of instruction
- Czech
- Further Comments
- Study Materials
The course can also be completed outside the examination period.
The course is taught annually.
C8855 Computational Chemistry and Molecular Modeling II
Faculty of ScienceSpring 2010
- Extent and Intensity
- 1/0/0. 2 credit(s). Recommended Type of Completion: k (colloquium). Other types of completion: zk (examination).
- Teacher(s)
- prof. RNDr. Jaroslav Koča, DrSc. (lecturer)
Mgr. Zdeněk Kříž, Ph.D. (lecturer) - Guaranteed by
- prof. RNDr. Jaroslav Koča, DrSc.
National Centre for Biomolecular Research – Faculty of Science
Contact Person: prof. RNDr. Jaroslav Koča, DrSc. - Timetable
- Fri 11:00–11:50 C04/211
- Prerequisites
- Basic level of general and physical chemistry. A basic knowledge in quantum chemistry is an advantage. It is strongly suggested that the student went through the course C7790/C7800. It is likely that the course is mainly for PhD students.
- Course Enrolment Limitations
- The course is also offered to the students of the fields other than those the course is directly associated with.
- fields of study / plans the course is directly associated with
- there are 21 fields of study the course is directly associated with, display
- Course objectives
- At the end of the course students should have basic knowledge in the field of computational chemistry. Basic knowledge about methods to analyze complicated energy functions will be gained together with knowledge about molecular dynamics simulations and studies on molecular complexes and chemical reactions. Also methods how to include solvent are discussed. Practical part of the course is oriented to work with an existing program package.
- Syllabus
- 1. Potential Energy Hypersurfaces. Stationary points and basic algorithms to search for them. 2. Simulation methods - molecular dynamics and Monte Carlo. 3. Conformational analysis in computational chemistry. 4. Computational chemistry of supramoleculas, molecular complexes and biomolecules. Docking. Designing of new molecules. 5. Solvent modeling. 6. Chemical reactions modeling. 7. Program systems Insight II, AMBER, DISCOVER, Oxford Molecular, WHATIF, AUTODOCK.
- Literature
- Lipkowitz, K B - Boyd, D B. Reviews in Computational Chemistry 1-9. New York : VCH Publishers, 1998.
- JENSEN, Frank. Introduction to Computational Chemistry. New York: J. Wiley & Sons Ltd., 1999. info
- HEHRE, Warren J., Alan J. SHUSTERMAN and W. Wayne HUANG. A laboratory book of computational organic chemistry. Irvine, Calif.: Wavefunction, 1996, xiv, 291 s. ISBN 0-9643495-5-8. info
- FORESMAN, J B and A FRISCH. Exploring Chemistry with Electronic Structure Methods. Pittsburgh: Gaussian, Inc., 1996. info
- Teaching methods
- Lectures combined with discussions.
- Assessment methods
- Oral examination
- Language of instruction
- Czech
- Further Comments
- The course can also be completed outside the examination period.
The course is taught annually.
C8855 Computational Chemistry and Molecular Modeling II
Faculty of ScienceSpring 2009
- Extent and Intensity
- 1/0/0. 2 credit(s). Recommended Type of Completion: k (colloquium). Other types of completion: zk (examination).
- Teacher(s)
- prof. RNDr. Jaroslav Koča, DrSc. (lecturer)
Mgr. Zdeněk Kříž, Ph.D. (lecturer) - Guaranteed by
- prof. RNDr. Jaroslav Koča, DrSc.
National Centre for Biomolecular Research – Faculty of Science
Contact Person: prof. RNDr. Jaroslav Koča, DrSc. - Timetable
- Fri 9:00–9:50 C04/211
- Prerequisites
- Basic level of general and physical chemistry. A basic knowledge in quantum chemistry is an advantage. It is strongly suggested that the student went through the course C7790/C7800. It is likely that the course is mainly for PhD students.
- Course Enrolment Limitations
- The course is also offered to the students of the fields other than those the course is directly associated with.
- fields of study / plans the course is directly associated with
- there are 21 fields of study the course is directly associated with, display
- Course objectives
- The course is oriented to obtaining basic knowledge in the field of computational chemistry. Basic knowledge about methods to analyze complicated energy functions will be gained together with knowledge about molecular dynamics simulations and studies on molecular complexes and chemical reactions. Also methods how to include solvent are discussed. Practical part of the course is oriented to work with an existing program package.
- Syllabus
- 1. Potential Energy Hypersurfaces. Stationary points and basic algorithms to search for them. 2. Simulation methods - molecular dynamics and Monte Carlo. 3. Conformational analysis in computational chemistry. 4. Computational chemistry of supramoleculas, molecular complexes and biomolecules. Docking. Designing of new molecules. 5. Solvent modeling. 6. Chemical reactions modeling. 7. Program systems Insight II, AMBER, DISCOVER, Oxford Molecular, WHATIF, AUTODOCK.
- Literature
- Lipkowitz, K B - Boyd, D B. Reviews in Computational Chemistry 1-9. New York : VCH Publishers, 1998.
- JENSEN, Frank. Introduction to Computational Chemistry. New York: J. Wiley & Sons Ltd., 1999. info
- HEHRE, Warren J., Alan J. SHUSTERMAN and W. Wayne HUANG. A laboratory book of computational organic chemistry. Irvine, Calif.: Wavefunction, 1996, xiv, 291 s. ISBN 0-9643495-5-8. info
- FORESMAN, J B and A FRISCH. Exploring Chemistry with Electronic Structure Methods. Pittsburgh: Gaussian, Inc., 1996. info
- Assessment methods
- Oral examination
- Language of instruction
- Czech
- Further Comments
- The course can also be completed outside the examination period.
The course is taught annually.
C8855 Computational Chemistry and Molecular Modeling II
Faculty of ScienceSpring 2008
- Extent and Intensity
- 1/0/0. 2 credit(s). Recommended Type of Completion: k (colloquium). Other types of completion: zk (examination).
- Teacher(s)
- prof. RNDr. Jaroslav Koča, DrSc. (lecturer)
Mgr. Zdeněk Kříž, Ph.D. (lecturer) - Guaranteed by
- prof. RNDr. Jaroslav Koča, DrSc.
National Centre for Biomolecular Research – Faculty of Science
Contact Person: prof. RNDr. Jaroslav Koča, DrSc. - Prerequisites
- Basic level of general and physical chemistry. A basic knowledge in quantum chemistry is an advantage. It is strongly suggested that the student went through the course C7790/C7800. It is likely that the course is mainly for PhD students.
- Course Enrolment Limitations
- The course is also offered to the students of the fields other than those the course is directly associated with.
- fields of study / plans the course is directly associated with
- there are 21 fields of study the course is directly associated with, display
- Course objectives (in Czech)
- Kurs je zaměřen na získání pokročilých znalostí v oblasti výpočetní chemie. Jeho orientace je výrazně aplikační. Student získá přehled o metodách analýzy komplikovaných energetických prostorů, metodách simulujících dynamiku molekul, metodách umožňujících studovat molekulární komplexy a chemické reakce. V neposlední řadě se student seznámí s různými způsoby, jak do výpočtu zahrnout solvent. V závěru se studenti seznámí s některým uživatelsky příjemným programovým balíkem pro počítačové modelování molekul a molekulárních systémů.
- Syllabus (in Czech)
- 1. Hyperplochy potenciální energie (PES). Význam a charakteristika stacionárních bodů. Základní algoritmy pro jejich vyhledávání. 2. Simulace chování molekulárního systému. Molekulová dynamika a metody Monte Carlo. 3. Konformační změny a jejich počítačové studium. Řešení problému mnohonásobných minim v konformační analýze. Energetické bariery konformačních interkonverzí. 4. Úvod do počítačového studia supramolekul , molekulárních komplexů a biomolekul. Dokování molekul. Design nových molekul. 5. Modelování solventu. 6. Modelování chemických reakcí. 7. Programové systémy Insight II, AMBER, DISCOVER, Oxford Molecular, WHATIF, AUTODOCK.
- Literature
- Lipkowitz, K B - Boyd, D B. Reviews in Computational Chemistry 1-9. New York : VCH Publishers, 1998.
- JENSEN, Frank. Introduction to Computational Chemistry. New York: J. Wiley & Sons Ltd., 1999. info
- HEHRE, Warren J., Alan J. SHUSTERMAN and W. Wayne HUANG. A laboratory book of computational organic chemistry. Irvine, Calif.: Wavefunction, 1996, xiv, 291 s. ISBN 0-9643495-5-8. info
- FORESMAN, J B and A FRISCH. Exploring Chemistry with Electronic Structure Methods. Pittsburgh: Gaussian, Inc., 1996. info
- Assessment methods (in Czech)
- Kurs sestává ze sedmi dvouhodinových přednášek. Ty jsou přednášeny samotnými frekventanty kursu na základě předběžné domluvy s vyučujícím. Pro ty studenty, kteří si zapsali cvičení, pak následuje samostatný projekt, který má ve většině případů úzký vztah k odbornému zaměření studenta.
- Language of instruction
- Czech
- Further Comments
- The course can also be completed outside the examination period.
The course is taught annually.
The course is taught: every week.
C8855 Computational Chemistry and Molecular Modeling II
Faculty of ScienceSpring 2007
- Extent and Intensity
- 1/0/0. 1 credit(s) (fasci plus compl plus > 4). Recommended Type of Completion: k (colloquium). Other types of completion: zk (examination).
- Teacher(s)
- prof. RNDr. Jaroslav Koča, DrSc. (lecturer)
Zdeněk Kříž (lecturer), prof. RNDr. Jaroslav Koča, DrSc. (deputy) - Guaranteed by
- prof. RNDr. Jaroslav Koča, DrSc.
National Centre for Biomolecular Research – Faculty of Science
Contact Person: prof. RNDr. Jaroslav Koča, DrSc. - Timetable
- Tue 13:00–13:50 C04/211
- Prerequisites
- Basic level of general and physical chemistry. A basic knowledge in quantum chemistry is an advantage. It is strongly suggested that the student went through the course C7790/C7800. It is likely that the course is mainly for PhD students.
- Course Enrolment Limitations
- The course is also offered to the students of the fields other than those the course is directly associated with.
- fields of study / plans the course is directly associated with
- there are 23 fields of study the course is directly associated with, display
- Course objectives (in Czech)
- Kurs je zaměřen na získání pokročilých znalostí v oblasti výpočetní chemie. Jeho orientace je výrazně aplikační. Student získá přehled o metodách analýzy komplikovaných energetických prostorů, metodách simulujících dynamiku molekul, metodách umožňujících studovat molekulární komplexy a chemické reakce. V neposlední řadě se student seznámí s různými způsoby, jak do výpočtu zahrnout solvent. V závěru se studenti seznámí s některým uživatelsky příjemným programovým balíkem pro počítačové modelování molekul a molekulárních systémů.
- Syllabus (in Czech)
- 1. Hyperplochy potenciální energie (PES). Význam a charakteristika stacionárních bodů. Základní algoritmy pro jejich vyhledávání. 2. Simulace chování molekulárního systému. Molekulová dynamika a metody Monte Carlo. 3. Konformační změny a jejich počítačové studium. Řešení problému mnohonásobných minim v konformační analýze. Energetické bariery konformačních interkonverzí. 4. Úvod do počítačového studia supramolekul , molekulárních komplexů a biomolekul. Dokování molekul. Design nových molekul. 5. Modelování solventu. 6. Modelování chemických reakcí. 7. Programové systémy Insight II, AMBER, DISCOVER, Oxford Molecular, WHATIF, AUTODOCK.
- Literature
- Lipkowitz, K B - Boyd, D B. Reviews in Computational Chemistry 1-9. New York : VCH Publishers, 1998.
- JENSEN, Frank. Introduction to Computational Chemistry. New York: J. Wiley & Sons Ltd., 1999. info
- HEHRE, Warren J., Alan J. SHUSTERMAN and W. Wayne HUANG. A laboratory book of computational organic chemistry. Irvine, Calif.: Wavefunction, 1996, xiv, 291 s. ISBN 0-9643495-5-8. info
- FORESMAN, J B and A FRISCH. Exploring Chemistry with Electronic Structure Methods. Pittsburgh: Gaussian, Inc., 1996. info
- Assessment methods (in Czech)
- Kurs sestává ze sedmi dvouhodinových přednášek. Ty jsou přednášeny samotnými frekventanty kursu na základě předběžné domluvy s vyučujícím. Pro ty studenty, kteří si zapsali cvičení, pak následuje samostatný projekt, který má ve většině případů úzký vztah k odbornému zaměření studenta.
- Language of instruction
- Czech
- Further Comments
- The course can also be completed outside the examination period.
The course is taught annually.
C8855 Computational Chemistry and Molecular Modeling II
Faculty of ScienceSpring 2006
- Extent and Intensity
- 1/0/0. 1 credit(s) (fasci plus compl plus > 4). Recommended Type of Completion: k (colloquium). Other types of completion: zk (examination).
- Teacher(s)
- prof. RNDr. Jaroslav Koča, DrSc. (lecturer)
Zdeněk Kříž (lecturer), prof. RNDr. Jaroslav Koča, DrSc. (deputy) - Guaranteed by
- prof. RNDr. Jaroslav Koča, DrSc.
National Centre for Biomolecular Research – Faculty of Science
Contact Person: prof. RNDr. Jaroslav Koča, DrSc. - Prerequisites
- Basic level of general and physical chemistry. A basic knowledge in quantum chemistry is an advantage. It is strongly suggested that the student went through the course C7790/C7800. It is likely that the course is mainly for PhD students.
- Course Enrolment Limitations
- The course is also offered to the students of the fields other than those the course is directly associated with.
- fields of study / plans the course is directly associated with
- there are 23 fields of study the course is directly associated with, display
- Course objectives (in Czech)
- Kurs je zaměřen na získání pokročilých znalostí v oblasti výpočetní chemie. Jeho orientace je výrazně aplikační. Student získá přehled o metodách analýzy komplikovaných energetických prostorů, metodách simulujících dynamiku molekul, metodách umožňujících studovat molekulární komplexy a chemické reakce. V neposlední řadě se student seznámí s různými způsoby, jak do výpočtu zahrnout solvent. V závěru se studenti seznámí s některým uživatelsky příjemným programovým balíkem pro počítačové modelování molekul a molekulárních systémů.
- Syllabus (in Czech)
- 1. Hyperplochy potenciální energie (PES). Význam a charakteristika stacionárních bodů. Základní algoritmy pro jejich vyhledávání. 2. Simulace chování molekulárního systému. Molekulová dynamika a metody Monte Carlo. 3. Konformační změny a jejich počítačové studium. Řešení problému mnohonásobných minim v konformační analýze. Energetické bariery konformačních interkonverzí. 4. Úvod do počítačového studia supramolekul , molekulárních komplexů a biomolekul. Dokování molekul. Design nových molekul. 5. Modelování solventu. 6. Modelování chemických reakcí. 7. Programové systémy Insight II, AMBER, DISCOVER, Oxford Molecular, WHATIF, AUTODOCK.
- Literature
- Lipkowitz, K B - Boyd, D B. Reviews in Computational Chemistry 1-9. New York : VCH Publishers, 1998.
- JENSEN, Frank. Introduction to Computational Chemistry. New York: J. Wiley & Sons Ltd., 1999. info
- HEHRE, Warren J., Alan J. SHUSTERMAN and W. Wayne HUANG. A laboratory book of computational organic chemistry. Irvine, Calif.: Wavefunction, 1996, xiv, 291 s. ISBN 0-9643495-5-8. info
- FORESMAN, J B and A FRISCH. Exploring Chemistry with Electronic Structure Methods. Pittsburgh: Gaussian, Inc., 1996. info
- Assessment methods (in Czech)
- Kurs sestává ze sedmi dvouhodinových přednášek. Ty jsou přednášeny samotnými frekventanty kursu na základě předběžné domluvy s vyučujícím. Pro ty studenty, kteří si zapsali cvičení, pak následuje samostatný projekt, který má ve většině případů úzký vztah k odbornému zaměření studenta.
- Language of instruction
- Czech
- Further Comments
- The course can also be completed outside the examination period.
The course is taught annually.
The course is taught: every week.
C8855 Computational Chemistry and Molecular Modeling II
Faculty of ScienceSpring 2005
- Extent and Intensity
- 1/0/0. 1 credit(s) (fasci plus compl plus > 4). Recommended Type of Completion: k (colloquium). Other types of completion: zk (examination).
- Teacher(s)
- prof. RNDr. Jaroslav Koča, DrSc. (lecturer)
Zdeněk Kříž (lecturer), prof. RNDr. Jaroslav Koča, DrSc. (deputy) - Guaranteed by
- prof. RNDr. Jaroslav Koča, DrSc.
Chemistry Section – Faculty of Science
Contact Person: prof. RNDr. Jaroslav Koča, DrSc. - Prerequisites
- Basic level of general and physical chemistry. A basic knowledge in quantum chemistry is an advantage. It is strongly suggested that the student went through the course C7790/C7800. It is likely that the course is mainly for PhD students.
- Course Enrolment Limitations
- The course is also offered to the students of the fields other than those the course is directly associated with.
- fields of study / plans the course is directly associated with
- there are 23 fields of study the course is directly associated with, display
- Course objectives (in Czech)
- Kurs je zaměřen na získání pokročilých znalostí v oblasti výpočetní chemie. Jeho orientace je výrazně aplikační. Student získá přehled o metodách analýzy komplikovaných energetických prostorů, metodách simulujících dynamiku molekul, metodách umožňujících studovat molekulární komplexy a chemické reakce. V neposlední řadě se student seznámí s různými způsoby, jak do výpočtu zahrnout solvent. V závěru se studenti seznámí s některým uživatelsky příjemným programovým balíkem pro počítačové modelování molekul a molekulárních systémů.
- Syllabus (in Czech)
- 1. Hyperplochy potenciální energie (PES). Význam a charakteristika stacionárních bodů. Základní algoritmy pro jejich vyhledávání. 2. Simulace chování molekulárního systému. Molekulová dynamika a metody Monte Carlo. 3. Konformační změny a jejich počítačové studium. Řešení problému mnohonásobných minim v konformační analýze. Energetické bariery konformačních interkonverzí. 4. Úvod do počítačového studia supramolekul , molekulárních komplexů a biomolekul. Dokování molekul. Design nových molekul. 5. Modelování solventu. 6. Modelování chemických reakcí. 7. Programové systémy Insight II, AMBER, DISCOVER, Oxford Molecular, WHATIF, AUTODOCK.
- Literature
- Lipkowitz, K B - Boyd, D B. Reviews in Computational Chemistry 1-9. New York : VCH Publishers, 1998.
- JENSEN, Frank. Introduction to Computational Chemistry. New York: J. Wiley & Sons Ltd., 1999. info
- HEHRE, Warren J., Alan J. SHUSTERMAN and W. Wayne HUANG. A laboratory book of computational organic chemistry. Irvine, Calif.: Wavefunction, 1996, xiv, 291 s. ISBN 0-9643495-5-8. info
- FORESMAN, J B and A FRISCH. Exploring Chemistry with Electronic Structure Methods. Pittsburgh: Gaussian, Inc., 1996. info
- Assessment methods (in Czech)
- Kurs sestává ze sedmi dvouhodinových přednášek. Ty jsou přednášeny samotnými frekventanty kursu na základě předběžné domluvy s vyučujícím. Pro ty studenty, kteří si zapsali cvičení, pak následuje samostatný projekt, který má ve většině případů úzký vztah k odbornému zaměření studenta.
- Language of instruction
- Czech
- Further Comments
- The course can also be completed outside the examination period.
The course is taught annually.
The course is taught: every week.
C8855 Computational Chemistry and Molecular Modeling II
Faculty of ScienceSpring 2004
- Extent and Intensity
- 1/0/0. 1 credit(s) (fasci plus compl plus > 4). Recommended Type of Completion: k (colloquium). Other types of completion: zk (examination).
- Teacher(s)
- prof. RNDr. Jaroslav Koča, DrSc. (lecturer)
Mgr. Zdeněk Kříž, Ph.D. (seminar tutor) - Guaranteed by
- prof. RNDr. Jaroslav Koča, DrSc.
Chemistry Section – Faculty of Science
Contact Person: prof. RNDr. Jaroslav Koča, DrSc. - Prerequisites
- Basic level of general and physical chemistry. A basic knowledge in quantum chemistry is an advantage. It is strongly suggested that the student went through the course C7790/C7800. It is likely that the course is mainly for PhD students.
- Course Enrolment Limitations
- The course is also offered to the students of the fields other than those the course is directly associated with.
The capacity limit for the course is 10 student(s).
Current registration and enrolment status: enrolled: 0/10, only registered: 0/10, only registered with preference (fields directly associated with the programme): 0/10 - fields of study / plans the course is directly associated with
- there are 21 fields of study the course is directly associated with, display
- Course objectives (in Czech)
- Kurs je zaměřen na získání pokročilých znalostí v oblasti výpočetní chemie. Jeho orientace je výrazně aplikační. Student získá přehled o metodách analýzy komplikovaných energetických prostorů, metodách simulujících dynamiku molekul, metodách umožňujících studovat molekulární komplexy a chemické reakce. V neposlední řadě se student seznámí s různými způsoby, jak do výpočtu zahrnout solvent. V závěru se studenti seznámí s některým uživatelsky příjemným programovým balíkem pro počítačové modelování molekul a molekulárních systémů.
- Syllabus (in Czech)
- 1. Hyperplochy potenciální energie (PES). Význam a charakteristika stacionárních bodů. Základní algoritmy pro jejich vyhledávání. 2. Simulace chování molekulárního systému. Molekulová dynamika a metody Monte Carlo. 3. Konformační změny a jejich počítačové studium. Řešení problému mnohonásobných minim v konformační analýze. Energetické bariery konformačních interkonverzí. 4. Úvod do počítačového studia supramolekul , molekulárních komplexů a biomolekul. Dokování molekul. Design nových molekul. 5. Modelování solventu. 6. Modelování chemických reakcí. 7. Programové systémy Insight II, AMBER, DISCOVER, Oxford Molecular, WHATIF, AUTODOCK.
- Literature
- Lipkowitz, K B - Boyd, D B. Reviews in Computational Chemistry 1-9. New York : VCH Publishers, 1998.
- JENSEN, Frank. Introduction to Computational Chemistry. New York: J. Wiley & Sons Ltd., 1999. info
- HEHRE, Warren J., Alan J. SHUSTERMAN and W. Wayne HUANG. A laboratory book of computational organic chemistry. Irvine, Calif.: Wavefunction, 1996, xiv, 291 s. ISBN 0-9643495-5-8. info
- FORESMAN, J B and A FRISCH. Exploring Chemistry with Electronic Structure Methods. Pittsburgh: Gaussian, Inc., 1996. info
- Assessment methods (in Czech)
- Kurs sestává ze sedmi dvouhodinových přednášek. Ty jsou přednášeny samotnými frekventanty kursu na základě předběžné domluvy s vyučujícím. Pro ty studenty, kteří si zapsali cvičení, pak následuje samostatný projekt, který má ve většině případů úzký vztah k odbornému zaměření studenta.
- Language of instruction
- Czech
- Further Comments
- The course can also be completed outside the examination period.
The course is taught annually.
The course is taught: every week.
C8855 Computational Chemistry and Molecular Modeling II
Faculty of ScienceSpring 2003
- Extent and Intensity
- 1/0/0. 1 credit(s) (fasci plus compl plus > 4). Recommended Type of Completion: k (colloquium). Other types of completion: zk (examination).
- Teacher(s)
- prof. RNDr. Jaroslav Koča, DrSc. (lecturer)
Zdeněk Kříž (lecturer), prof. RNDr. Jaroslav Koča, DrSc. (deputy) - Guaranteed by
- prof. RNDr. Jaroslav Koča, DrSc.
Chemistry Section – Faculty of Science
Contact Person: prof. RNDr. Jaroslav Koča, DrSc. - Prerequisites
- Basic level of general and physical chemistry. A basic knowledge in quantum chemistry is an advantage. It is strongly suggested that the student went through the course C7790/C7800. It is likely that the course is mainly for PhD students.
- Course Enrolment Limitations
- The course is also offered to the students of the fields other than those the course is directly associated with.
- fields of study / plans the course is directly associated with
- there are 23 fields of study the course is directly associated with, display
- Course objectives (in Czech)
- Kurs je zaměřen na získání pokročilých znalostí v oblasti výpočetní chemie. Jeho orientace je výrazně aplikační. Student získá přehled o metodách analýzy komplikovaných energetických prostorů, metodách simulujících dynamiku molekul, metodách umožňujících studovat molekulární komplexy a chemické reakce. V neposlední řadě se student seznámí s různými způsoby, jak do výpočtu zahrnout solvent. V závěru se studenti seznámí s některým uživatelsky příjemným programovým balíkem pro počítačové modelování molekul a molekulárních systémů.
- Syllabus (in Czech)
- 1. Hyperplochy potenciální energie (PES). Význam a charakteristika stacionárních bodů. Základní algoritmy pro jejich vyhledávání. 2. Simulace chování molekulárního systému. Molekulová dynamika a metody Monte Carlo. 3. Konformační změny a jejich počítačové studium. Řešení problému mnohonásobných minim v konformační analýze. Energetické bariery konformačních interkonverzí. 4. Úvod do počítačového studia supramolekul , molekulárních komplexů a biomolekul. Dokování molekul. Design nových molekul. 5. Modelování solventu. 6. Modelování chemických reakcí. 7. Programové systémy Insight II, AMBER, DISCOVER, Oxford Molecular, WHATIF, AUTODOCK.
- Literature
- Lipkowitz, K B - Boyd, D B. Reviews in Computational Chemistry 1-9. New York : VCH Publishers, 1998.
- JENSEN, Frank. Introduction to Computational Chemistry. New York: J. Wiley & Sons Ltd., 1999. info
- HEHRE, Warren J., Alan J. SHUSTERMAN and W. Wayne HUANG. A laboratory book of computational organic chemistry. Irvine, Calif.: Wavefunction, 1996, xiv, 291 s. ISBN 0-9643495-5-8. info
- FORESMAN, J B and A FRISCH. Exploring Chemistry with Electronic Structure Methods. Pittsburgh: Gaussian, Inc., 1996. info
- Assessment methods (in Czech)
- Kurs sestává ze sedmi dvouhodinových přednášek. Ty jsou přednášeny samotnými frekventanty kursu na základě předběžné domluvy s vyučujícím. Pro ty studenty, kteří si zapsali cvičení, pak následuje samostatný projekt, který má ve většině případů úzký vztah k odbornému zaměření studenta.
- Language of instruction
- Czech
- Further Comments
- The course can also be completed outside the examination period.
The course is taught annually.
The course is taught: every week.
C8855 Computational Chemistry and Molecular Modeling II
Faculty of ScienceSpring 2002
- Extent and Intensity
- 1/0/0. 2 credit(s). Recommended Type of Completion: zk (examination). Other types of completion: k (colloquium).
- Teacher(s)
- prof. RNDr. Jaroslav Koča, DrSc. (lecturer)
Zdeněk Kříž (lecturer), prof. RNDr. Jaroslav Koča, DrSc. (deputy) - Guaranteed by
- prof. RNDr. Jaroslav Koča, DrSc.
Chemistry Section – Faculty of Science - Course Enrolment Limitations
- The course is also offered to the students of the fields other than those the course is directly associated with.
- fields of study / plans the course is directly associated with
- there are 23 fields of study the course is directly associated with, display
- Language of instruction
- Czech
- Further Comments
- The course can also be completed outside the examination period.
The course is taught annually.
The course is taught: every week.
C8855 Computational Chemistry and Molecular Modeling II
Faculty of Sciencespring 2012 - acreditation
The information about the term spring 2012 - acreditation is not made public
- Extent and Intensity
- 1/0/0. 2 credit(s). Recommended Type of Completion: k (colloquium). Other types of completion: zk (examination).
- Teacher(s)
- prof. RNDr. Jaroslav Koča, DrSc. (lecturer)
Mgr. Zdeněk Kříž, Ph.D. (lecturer) - Guaranteed by
- prof. RNDr. Jaroslav Koča, DrSc.
National Centre for Biomolecular Research – Faculty of Science
Contact Person: prof. RNDr. Jaroslav Koča, DrSc.
Supplier department: National Centre for Biomolecular Research – Faculty of Science - Prerequisites
- Basic level of general and physical chemistry. A basic knowledge in quantum chemistry is an advantage. It is strongly suggested that the student went through the course C7790/C7800. It is likely that the course is mainly for PhD students.
- Course Enrolment Limitations
- The course is also offered to the students of the fields other than those the course is directly associated with.
- fields of study / plans the course is directly associated with
- there are 21 fields of study the course is directly associated with, display
- Course objectives
- At the end of the course students should have basic knowledge in the field of computational chemistry. Basic knowledge about methods to analyze complicated energy functions will be gained together with knowledge about molecular dynamics simulations and studies on molecular complexes and chemical reactions. Also methods how to include solvent are discussed. Practical part of the course is oriented to work with an existing program package.
- Syllabus
- 1. Potential Energy Hypersurfaces. Stationary points and basic algorithms to search for them. 2. Simulation methods - molecular dynamics and Monte Carlo. 3. Conformational analysis in computational chemistry. 4. Computational chemistry of supramoleculas, molecular complexes and biomolecules. Docking. Designing of new molecules. 5. Solvent modeling. 6. Chemical reactions modeling. 7. Program systems Insight II, AMBER, DISCOVER, Oxford Molecular, WHATIF, AUTODOCK.
- Literature
- Lipkowitz, K B - Boyd, D B. Reviews in Computational Chemistry 1-9. New York : VCH Publishers, 1998.
- JENSEN, Frank. Introduction to Computational Chemistry. New York: J. Wiley & Sons Ltd., 1999. info
- HEHRE, Warren J., Alan J. SHUSTERMAN and W. Wayne HUANG. A laboratory book of computational organic chemistry. Irvine, Calif.: Wavefunction, 1996, xiv, 291 s. ISBN 0-9643495-5-8. info
- FORESMAN, J B and A FRISCH. Exploring Chemistry with Electronic Structure Methods. Pittsburgh: Gaussian, Inc., 1996. info
- Teaching methods
- Lectures combined with discussions.
- Assessment methods
- Oral examination
- Language of instruction
- Czech
- Further Comments
- The course can also be completed outside the examination period.
The course is taught annually.
The course is taught: every week.
C8855 Computational Chemistry and Molecular Modeling II
Faculty of ScienceSpring 2011 - only for the accreditation
- Extent and Intensity
- 1/0/0. 2 credit(s). Recommended Type of Completion: k (colloquium). Other types of completion: zk (examination).
- Teacher(s)
- prof. RNDr. Jaroslav Koča, DrSc. (lecturer)
Mgr. Zdeněk Kříž, Ph.D. (lecturer) - Guaranteed by
- prof. RNDr. Jaroslav Koča, DrSc.
National Centre for Biomolecular Research – Faculty of Science
Contact Person: prof. RNDr. Jaroslav Koča, DrSc. - Prerequisites
- Basic level of general and physical chemistry. A basic knowledge in quantum chemistry is an advantage. It is strongly suggested that the student went through the course C7790/C7800. It is likely that the course is mainly for PhD students.
- Course Enrolment Limitations
- The course is also offered to the students of the fields other than those the course is directly associated with.
- fields of study / plans the course is directly associated with
- there are 21 fields of study the course is directly associated with, display
- Course objectives
- At the end of the course students should have basic knowledge in the field of computational chemistry. Basic knowledge about methods to analyze complicated energy functions will be gained together with knowledge about molecular dynamics simulations and studies on molecular complexes and chemical reactions. Also methods how to include solvent are discussed. Practical part of the course is oriented to work with an existing program package.
- Syllabus
- 1. Potential Energy Hypersurfaces. Stationary points and basic algorithms to search for them. 2. Simulation methods - molecular dynamics and Monte Carlo. 3. Conformational analysis in computational chemistry. 4. Computational chemistry of supramoleculas, molecular complexes and biomolecules. Docking. Designing of new molecules. 5. Solvent modeling. 6. Chemical reactions modeling. 7. Program systems Insight II, AMBER, DISCOVER, Oxford Molecular, WHATIF, AUTODOCK.
- Literature
- Lipkowitz, K B - Boyd, D B. Reviews in Computational Chemistry 1-9. New York : VCH Publishers, 1998.
- JENSEN, Frank. Introduction to Computational Chemistry. New York: J. Wiley & Sons Ltd., 1999. info
- HEHRE, Warren J., Alan J. SHUSTERMAN and W. Wayne HUANG. A laboratory book of computational organic chemistry. Irvine, Calif.: Wavefunction, 1996, xiv, 291 s. ISBN 0-9643495-5-8. info
- FORESMAN, J B and A FRISCH. Exploring Chemistry with Electronic Structure Methods. Pittsburgh: Gaussian, Inc., 1996. info
- Teaching methods
- Lectures combined with discussions.
- Assessment methods
- Oral examination
- Language of instruction
- Czech
- Further Comments
- The course can also be completed outside the examination period.
The course is taught annually.
The course is taught: every week.
C8855 Computational Chemistry and Molecular Modeling II
Faculty of ScienceSpring 2008 - for the purpose of the accreditation
- Extent and Intensity
- 1/0/0. 2 credit(s). Recommended Type of Completion: k (colloquium). Other types of completion: zk (examination).
- Teacher(s)
- prof. RNDr. Jaroslav Koča, DrSc. (lecturer)
Mgr. Zdeněk Kříž, Ph.D. (lecturer) - Guaranteed by
- prof. RNDr. Jaroslav Koča, DrSc.
National Centre for Biomolecular Research – Faculty of Science
Contact Person: prof. RNDr. Jaroslav Koča, DrSc. - Prerequisites
- Basic level of general and physical chemistry. A basic knowledge in quantum chemistry is an advantage. It is strongly suggested that the student went through the course C7790/C7800. It is likely that the course is mainly for PhD students.
- Course Enrolment Limitations
- The course is also offered to the students of the fields other than those the course is directly associated with.
- fields of study / plans the course is directly associated with
- there are 21 fields of study the course is directly associated with, display
- Course objectives (in Czech)
- Kurs je zaměřen na získání pokročilých znalostí v oblasti výpočetní chemie. Jeho orientace je výrazně aplikační. Student získá přehled o metodách analýzy komplikovaných energetických prostorů, metodách simulujících dynamiku molekul, metodách umožňujících studovat molekulární komplexy a chemické reakce. V neposlední řadě se student seznámí s různými způsoby, jak do výpočtu zahrnout solvent. V závěru se studenti seznámí s některým uživatelsky příjemným programovým balíkem pro počítačové modelování molekul a molekulárních systémů.
- Syllabus (in Czech)
- 1. Hyperplochy potenciální energie (PES). Význam a charakteristika stacionárních bodů. Základní algoritmy pro jejich vyhledávání. 2. Simulace chování molekulárního systému. Molekulová dynamika a metody Monte Carlo. 3. Konformační změny a jejich počítačové studium. Řešení problému mnohonásobných minim v konformační analýze. Energetické bariery konformačních interkonverzí. 4. Úvod do počítačového studia supramolekul , molekulárních komplexů a biomolekul. Dokování molekul. Design nových molekul. 5. Modelování solventu. 6. Modelování chemických reakcí. 7. Programové systémy Insight II, AMBER, DISCOVER, Oxford Molecular, WHATIF, AUTODOCK.
- Literature
- Lipkowitz, K B - Boyd, D B. Reviews in Computational Chemistry 1-9. New York : VCH Publishers, 1998.
- JENSEN, Frank. Introduction to Computational Chemistry. New York: J. Wiley & Sons Ltd., 1999. info
- HEHRE, Warren J., Alan J. SHUSTERMAN and W. Wayne HUANG. A laboratory book of computational organic chemistry. Irvine, Calif.: Wavefunction, 1996, xiv, 291 s. ISBN 0-9643495-5-8. info
- FORESMAN, J B and A FRISCH. Exploring Chemistry with Electronic Structure Methods. Pittsburgh: Gaussian, Inc., 1996. info
- Assessment methods (in Czech)
- Kurs sestává ze sedmi dvouhodinových přednášek. Ty jsou přednášeny samotnými frekventanty kursu na základě předběžné domluvy s vyučujícím. Pro ty studenty, kteří si zapsali cvičení, pak následuje samostatný projekt, který má ve většině případů úzký vztah k odbornému zaměření studenta.
- Language of instruction
- Czech
- Further Comments
- The course can also be completed outside the examination period.
The course is taught annually.
The course is taught: every week.
- Enrolment Statistics (recent)