[gmx-users] checking oplsaa parameters in the .top file
rob yang
nextgame at hotmail.com
Thu Feb 23 23:39:32 CET 2006
Hi list,
I have generated a .top file for my molecule (non-protein) using the oplsaa
format. Here's a snip of what the .top file looks like:
_BEGIN SNIP
[ atoms ]
; id at type res nr residu name at name cg nr charge
1 opls_135 1 BAL C 1 -0.180
2 opls_140 1 BAL H 1 0.060
3 opls_140 1 BAL H 1 0.060
4 opls_140 1 BAL H 1 0.060
...
[dihedrals]
1 5 7 8 3
...
_END SNIP
I am guessing that the actual torsion parameters are generated based on the
oplsaa_id corresponding to each atom index. Is there a way for me to
actually see which parameters are generated? In particular, the gromos .top
files usually contain the information:
_BEGIN SNIP
...
[dihedrals]
2 1 5 9 1 gd_29
..
_END SNIP
so I know gd_29 is assigned to these 4 atoms. How would I obtain that
information from the oplsaa .top files?
Thank you very much in advance.
Rob
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