Difference between revisions of "Global optimization of biomolecules using AMBER9"
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1. ''coords.inpcrd'' -- file with coordinates |
1. ''coords.inpcrd'' -- file with coordinates |
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| − | 2. ''coords.prmtop'' -- topology file (see |
+ | 2. ''coords.prmtop'' -- topology file (see [http://wwmm.ch.cam.ac.uk/wikis/cuc3/index.php/Perm-prmtop.py here]) |
3. ''min.in'' -- file with AMBER9 keywords describing the conditions for AMBER minimization of the studied system (however, we state to have one cycle only), e.g.: |
3. ''min.in'' -- file with AMBER9 keywords describing the conditions for AMBER minimization of the studied system (however, we state to have one cycle only), e.g.: |
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Revision as of 11:36, 1 May 2008
Here you can find examples of input files necessary to work with GMIN:
1. coords.inpcrd -- file with coordinates
2. coords.prmtop -- topology file (see here)
3. min.in -- file with AMBER9 keywords describing the conditions for AMBER minimization of the studied system (however, we state to have one cycle only), e.g.:
Minimization
&cntrl
imin=1, maxcyc=1, ncyc=1,
igb=2, saltcon=0.2,
ntx=1, ntb=0,
cut=999.0
/
4. min_cd.in -- this file controls conditions for molecular dynamics in AMBER9, e.g.:
STOP
&cntrl
imin = 0,
tempi = 500.0, temp0 = 700.0,
ntt = 3, gamma_ln = 1.0,
nstlim = 300, dt = 0.001,
igb = 2, saltcon = 0.2,
ntb = 0,
ntpr = 100, ntwx = 100, nrespa=1,
cut = 999.0
/
5. data -- file with GMIN keywords:
SLOPPYCONV 1.0D-6 TIGHTCONV 1.0D-7 MAXERISE 1.0D-4 MAXIT 100 600 MAXBFGS 1.0 SAVE 100 STEPS 1000 STEP 0.0 RADIUS 300 AMBERMDSTEPS AMBER9 coords.inpcrd inpcrd
Thats all!