Difference between revisions of "Minimizing a structure using OPTIM and AMBER9"
Jump to navigation
Jump to search
import>Em427 |
import>Em427 |
||
| Line 2: | Line 2: | ||
| + | To optimize geometry you need four (or five, see below) files with names specified in the following list: |
||
| − | There is a list of necessary files for optimization of geometry: |
||
1. ''coords.inpcrd'' -- file with coordinates in AMBER9 format |
1. ''coords.inpcrd'' -- file with coordinates in AMBER9 format |
||
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.