Difference between revisions of "Global optimization of biomolecules using AMBER9"
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cut = 999.0 |
cut = 999.0 |
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+ | 5. ''data'' -- file with GMIN keywords: |
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+ | SLOPPYCONV 1.0D-6 |
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+ | TIGHTCONV 1.0D-7 |
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+ | MAXERISE 1.0D-4 |
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+ | MAXIT 100 600 |
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+ | MAXBFGS 1.0 |
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+ | SAVE 100 |
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+ | STEPS 1000 |
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+ | STEP 0.0 |
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+ | RADIUS 300 |
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+ | AMBERMDSTEPS |
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+ | AMBER9 coords.inpcrd inpcrd |
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+ | |||
+ | Thats all! |
Revision as of 10:34, 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 Link 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!