Reference manuals
AMBER
Petr Kulhánek
kulhanek@chemi.muni.cz
National Center for Biomolecular Research, Faculty of Science Masaryk University, Kotlářská 2, CZ-61137 Brno
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AMBER
http://ambermd.org
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Flowchart, MD in vacuum
structure (Avogadro/ Nemesis)
input.mol2 ->
types and charges (antechamber)
visual inspection in a text editor
output.mol2
missing parameters (parmchk)
compilation of topology and default coordinates (tleap)
o
o
output.parm7 relax03.rst7
equilibration (pequijob, protocol vacOl)
equilibration at 300K
heating t 300K
optimalization
output.parm7 output.rst7
visual inspection in VMD
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Flowchart, vacuum,
output.parm7 relax03.rst7
visual inspection in VMD
V
l pre dyna
roduction amies 10 ns (sander)
output.parm7 prod.btraj
trajectory analysis in VMD
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1. Building a molecule
1. The molecule will be built in the program Avogadro/Nemesis.
2. The molecule geometry will be optimized (using force field MMFF94).
3. The optimized geometry will be saved in the format mol2 (input.mol2).
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2. Types, charges and FF para met*
Types and charges of individual atoms are determined by the program antechamber (module amber):
output file name input file name .
\ input file format \     0UtPut file format
$ module add amber ^ \ ^
$ antechamber -i input.mol2 -fi mol2 -o output.mol2 -fo mol2 \
-rn RES -nc 0 -c bcc
\
total charge      charge calculation method name of the residue (max. 3 characters)
line continuation
input file name
Missing parameters a\^ determined by the program parmchk (module amber):
$ parmchk -i output.mol2 -f mol2 -o output.frcmod
N
input file format « output file with missing parameters
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[3. Building a topology
Create a script (script.in) for the program tleap. The script describes how to build the final topology (contains a list of constraints, angles, dihedral angles and parameters of bonding and non-boding interactions) and system coordinates.
# loading parameters of force field (GAFF) source leaprc.gaff
# loading missing parameter loadamberparams output.frcmod
# loading template with structure LIG = loadmol2 output.mol2
# saving topology and coordinates saveamberparm LIG output.parm7 output.rst7
We will execute the script b
$ module add amber $ tleap -f script. ir7
/ the interpreter tleap:
go through the entire output displayed on the screen to see if an error has occurred somewhere
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[4. Equilibration
1. Make a separate directory and copy the output.parm7 and output.rst7 files there. Set the directory as the current directory.
2. Create templates for equilibration, use the protocol vacOl from the dynutil module.
$ module add dynutil $ small-prep vacOl
3. Open the file pequiJob in text editor and edit the items containing names of the topology and coordinate files.
# input topology --------------------------------------------------------------
# file name without path,  this file has to be presented in working directory export PEQUI_TOP="output.parm7"
# input coordinates -----------------------------------------------------------
# file name without path,  this file has to be presented in working directory export PEQUI_CRD="output.rst7"
4. Submit job pequiJob into the batch system.
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5. Production dynamics
1. Create a separate directory and copy output.parm7 and relax03.rst7 files there (result from equilibration). Set the directory as the current directory.
2. Copy the contents of the directory /home/kulhanek/Vibuch/2011/prod-vac to the
directory.
3. If other file names were used, it is necessary to edit the script prodJob .
4. Check the contents of the prod.in file.
5. Submit the job prodJob into the batch system.
The goal of the production dynamics is to create trajectory which is used for calculation of system properties.
We will display the resulting trajectory in the VMD program:
$ vmd -parm7 output.parm7 -netcdf prod.btraj
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5. Production dynamics,...
# production dynamics at 300 K
&cntrl imin=0,
nstlim=10000000, dt=0.001, irest=l, ntx=5,
control file prod.in determines under what conditions the production dynamics takes place
total number of steps
the size of the integration step (in ps)
ntpr=1000, ntwx=1000, ntwr=1000, ioutfm=l,
ntf=2, ntb=0, cut=999,
ig=-l,
temp0=300.0, ntt=3,
gamma_ln=2.0,
ntc=2, Send
temperature in K    Settings of Langevin thermostat
the meaning of other parameters can be found in the manual of sander program
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