Difference between revisions of "Minimizing a structure using OPTIM and AMBER9"
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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 (see description [http://wwmm.ch.cam.ac.uk/wikis/cuc3/index.php/Perm-prmtop.py here] |
3. ''min.in'' - file with AMBER9 keywords describing the conditions for molecular dynamics of the studied system, e.g.: |
3. ''min.in'' - file with AMBER9 keywords describing the conditions for molecular dynamics of the studied system, e.g.: |
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You still need to have a ''coords.inpcrd'' file in the same directory or OPTIM won't run! |
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'']). |
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Revision as of 13:54, 1 May 2008
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 (see description here
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 the 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!