Global optimization of biomolecules using AMBER9: Difference between revisions
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2. ''coords.prmtop'' -- topology file (see [[Link here]]) |
2. ''coords.prmtop'' -- topology file (see [[Link here]]) |
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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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3. ''min.in'' -- |
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Minimization |
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&cntrl |
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imin=1, maxcyc=1, ncyc=1, |
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igb=2, saltcon=0.2, |
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ntx=1, ntb=0, |
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cut=999.0 |
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/ |
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4. ''min_cd.in'' -- this file controls conditions for molecular dynamics in AMBER9, e.g.: |
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STOP |
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&cntrl |
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imin = 0, |
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tempi = 500.0, temp0 = 700.0, |
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ntt = 3, gamma_ln = 1.0, |
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nstlim = 300, dt = 0.001, |
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igb = 2, saltcon = 0.2, |
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ntb = 0, |
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ntpr = 100, ntwx = 100, nrespa=1, |
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cut = 999.0 |
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/ |
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Revision as of 10:31, 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
/