Difference between revisions of "Minimizing a structure using OPTIM and AMBER9"
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| − | To optimize geometry you need four (or five, see below) files with names specified in the following list: |
+ | To optimize a 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 |
1. ''coords.inpcrd'' -- file with coordinates in AMBER9 format |
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2. ''coords.prmtop'' -- AMBER9 topology file |
2. ''coords.prmtop'' -- AMBER9 topology file |
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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 the conditions for molecular dynamics of the studied system, e.g.: |
Minimization |
Minimization |
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AMBER9 coords.inpcrd inpcrd |
AMBER9 coords.inpcrd inpcrd |
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| − | If file |
+ | If file for the 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 |
AMBER9 start |
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| − | + | You still need to have a ''coords.inpcrd'' file in the same directory or OPTIM won't run! |
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Files ''coords.inpcrd'' and ''coords.prmtop'' are created by LEaP (program in AMBER package). In the case of ''coords.prmtop'', it is important to use the program ''perm-prmtop.py'' to obtain a topology file that is invariant to the permutation of chemically equivalent atoms or groups (see description of [http://wwmm.ch.cam.ac.uk/wikis/cuc3/index.php/Perm-prmtop.py ''perm-prmtop.py'']). |
Files ''coords.inpcrd'' and ''coords.prmtop'' are created by LEaP (program in AMBER package). In the case of ''coords.prmtop'', it is important to use the program ''perm-prmtop.py'' to obtain a topology file that is invariant to the permutation of chemically equivalent atoms or groups (see description of [http://wwmm.ch.cam.ac.uk/wikis/cuc3/index.php/Perm-prmtop.py ''perm-prmtop.py'']). |
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Revision as of 21:06, 30 April 2008
For users of AMBER9:
To optimize a 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 the conditions for molecular dynamics of the studied system, e.g.:
Minimization
&cntrl
imin=1, maxcyc=1, ncyc=1,
igb=2, saltcon=0.2,
ntx=1, ntb=0,
cut=15.0, rgbmax=12.0, ifswitch=1
/
4. odata -- file with OPTIM keywords specifying method of minimization, convergence criterion, etc. e.g.:
BFGSMIN 1.0D-6 BFGSSTEPS 10000 UPDATES 10 MAXERISE 1.0D-4 AMBER9 coords.inpcrd inpcrd
If file for the 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
You still need to have a coords.inpcrd file in the same directory or OPTIM won't run!
Files coords.inpcrd and coords.prmtop are created by LEaP (program in AMBER package). In the case of coords.prmtop, it is important to use the program perm-prmtop.py to obtain a topology file that is invariant to the permutation of chemically equivalent atoms or groups (see description of perm-prmtop.py).