[gmx-users] checking oplsaa parameters in the .top file

[Mark Abraham]

rob yang wrote:
> 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?

You can't from the .top files, because in [dihedrals] the .top file 
contains only the indices of the atoms involved in the dihedral, whose 
atom types can be looked up in [atoms]. Those atom types determine which 
dihedral function gets looked up from ffoplsaabon.itp, but that doesn't 
happen until you generate the .tpr file with grompp. The easiest thing 
to do is to generate the .tpr file and use gmxdump to inspect the 
results - remembering that the atom numbering you see there will start 
from zero, not one. You will see the above dihedral as a line in a 
dihedral section with 1 0 4 8 and then a index into a dihedral function 
array, which will be elsewhere in the output from gmxdump. You can, of 
course, check the calculation by hand by following the rules appropriate 
to OPLS-AA described in the manual & papers.

The gd_29 in gromos is probably pre-computed for some reason, and 
"#defined" in the gromos .itp files so that when grompp reads this .top 
file it expands gd_29 into whatever is actually useful.

Mark