Difference between revisions of "Minimizing a structure using OPTIM and AMBER9"
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import>Em427 |
import>Em427 |
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&cntrl |
&cntrl |
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imin=1, maxcyc=1, ncyc=1, |
imin=1, maxcyc=1, ncyc=1, |
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− | + | igb=2, saltcon=0.2, |
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− | ntx=1, ntb=0 |
+ | ntx=1, ntb=0, |
− | ifswitch=1 |
+ | cut=10.0, rgbmax=8.5, ifswitch=1 |
/ |
/ |
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MAXERISE 1.0D-4 |
MAXERISE 1.0D-4 |
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AMBER9 coords.inpcrd inpcrd |
AMBER9 coords.inpcrd inpcrd |
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+ | |||
+ | If file with starting geometry contains three columns with x, y, z coordinates, respectively, name this file ''start'' and change the last line of mentioned above ''odata'' file into: |
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+ | |||
+ | AMBER9 start |
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+ | |||
+ | Still you need to have ''coords.inpcrd'' file in the same directory. |
Revision as of 19:15, 30 April 2008
For users of AMBER9:
There is a list of necessary files:
1. coords.inpcrd -- file with coordinates in AMBER9 format
2. coords.prmtop -- AMBER9 topology file
3. min.in - file with AMBER9 keywords describing conditions for molecular dynamics of studied system, e.g.:
Minimization &cntrl imin=1, maxcyc=1, ncyc=1, igb=2, saltcon=0.2, ntx=1, ntb=0, cut=10.0, rgbmax=8.5, ifswitch=1 /
4. odata -- file with OPTIM keywords specifying method of minimization, convergence criterion, etc. e.g.:
BFGSMIN 1.0D-6 BFGSSTEPS 1000000 UPDATES 10000 MAXERISE 1.0D-4 AMBER9 coords.inpcrd inpcrd
If file with starting geometry contains three columns with x, y, z coordinates, respectively, name this file start and change the last line of mentioned above odata file into:
AMBER9 start
Still you need to have coords.inpcrd file in the same directory.