[gmx-users] Missing VdW Parameters

[darrellk at ece.ubc.ca]

Dear All,
I successfully ran the x2top command (x2top -ff select -f graphene_nm.gro
-o graphene_nm.top) and generated a topology using ffoplsaa, but my
topology is missing VdW parameters, which I thought should be appearing
in the [ pairs ] section of the topology file. I thought that x2top
would use the VdW parameters in ffoplsaanb.itp to populate the [ pairs ]
section of the topology file. But this appears not to be the case.
Please advise what may be the problem.

To help diagnose this problem, I am including a portion of the .gro file,
the relevant section of the .n2t file, and a portion of the [ pairs ]
section from the generated topology file.

selection from .gro file:
    2Grph C 1 0.000 0.000  0.000 0.0000 0.0000 0.0000
    2Grph C 2 0.071 -0.123 0.000 0.0000 0.0000 0.0000
    2Grph C 3 0.071 0.123  0.000 0.0000 0.0000 0.0000

relevant section of .n2t file:
C opls_145 0     12.011 3 C 0.140 C 0.140 C 0.140
C opls_145 -0.06 12.011 3 C 0.140 C 0.140 H 0.108
C opls_145 -0.12 12.011 3 C 0.140 H 0.108 H 0.108
H opls_146 0.06   1.008 1 C 0.108

selection from generated topology file:
[ pairs ]
; ai aj funct c0 c1 c2 c3
    1 11 1
    1 12 1
    1 13 1
    1 14 1

Much thanks in advance.

Darrell