Difference between revisions of "Minimizing a structure using OPTIM and AMBER9"
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import>Em427 |
import>Em427 |
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3. ''min.in'' - file with AMBER9 keywords describing conditions for molecular dynamics of studied system, e.g.: |
3. ''min.in'' - file with AMBER9 keywords describing conditions for molecular dynamics of studied system, e.g.: |
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| − | + | Minimization |
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| − | + | &cntrl |
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| − | imin=1, maxcyc=1, ncyc=1, |
+ | imin=1, maxcyc=1, ncyc=1, |
| − | igb=2, saltcon=0.2, |
+ | igb=2, saltcon=0.2, |
| − | ntx=1, ntb=0, |
+ | ntx=1, ntb=0, |
| − | cut=10.0, rgbmax=8.5, ifswitch=1 |
+ | cut=10.0, rgbmax=8.5, ifswitch=1 |
| − | / |
+ | / |
4. ''odata'' -- file with OPTIM keywords specifying method of minimization, convergence criterion, etc. e.g.: |
4. ''odata'' -- file with OPTIM keywords specifying method of minimization, convergence criterion, etc. e.g.: |
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| − | + | BFGSMIN 1.0D-6 |
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| − | + | BFGSSTEPS 1000000 |
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| − | + | UPDATES 10000 |
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| − | + | MAXERISE 1.0D-4 |
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| − | + | 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: |
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. |
Still you need to have ''coords.inpcrd'' file in the same directory. |
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Revision as of 19:18, 30 April 2008
For users of AMBER9:
To optimize geometry you need four (or five, see below) files with names specified in the following list:
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.