[gmx-users] OPLS-AA nonbonded force field format

[Shi Li]

Dear GMX users,

I am editing an OPLS-AA non-bonded itp file for my simulation system. I noticed in the ffoplsaa in gromacs folder, the non-bonded force field has following format:

[ atomtypes ]
; full atom descriptions are available in ffoplsaa.atp
; name  bond_type    mass    charge   ptype          sigma      epsilon
 opls_001   C   6      12.01100     0.500       A    3.75000e-01  4.39320e-01 ; SIG
…

However, the non-bonded format I find from the manual is like this:

 [ atomtypes ]
;name at.num mass charge ptype V(c6) W(c12)
 O 8 15.99940 0.000 A 0.22617E-02 0.74158E-06
OM 8 15.99940 0.000 A 0.22617E-02 0.74158E-06

The difference is in the manual, it doesn’t contain the first column, which I think is the atom name. When I built my own non bonded itp file, I try make my file looks like the first one. For example, if I have an atom name S1, and belongs to type “S”, my first line of the file looks like this:
[ atomtypes ]
; full atom descriptions are available in ffoplsaa.atp
; name  bond_type    mass    charge   ptype          sigma      epsilon
;   S1    S      16  32.0600     0.266702   A  0.3550    1.046700

However, this give me the error as followings:
Fatal error:
Atomtype S not found

This could be fixed if I remove the S1 column and make my file format likes the one in the manual. So, my question is, what is the correct non-bonded forcefield format for OPLS? If I don't specify the name of the atoms, I think they are specified in the topology file, under the [ atoms ], is that correct? In this case, how should the first format work in the grompp?

Another question about this non-bonded file is, I think I just need to specify the atom types, instead of every single atom in my molecule, is this correct? As I tried to include all the atoms in the nonbonded file, but it will give me the warning of override the atoms. But the format in opls seems to have all the atoms listed. In this case, how should I edit the non-bonded file correctly?

Thank you all very much!
Shi