[gmx-users] oplsaa force field

Dongsheng Zhang dong at pampas.chem.purdue.edu
Sun Jul 2 23:50:35 CEST 2006

Dear GMX users,

I'd like to use oplsaa FF format to build my own force field for my
project. After I finished it, I can use pdb2gmx. but not grompp. The
problem is from my **nb.itp file. I have specified some unusual (not
follow the combination rule) nonbonded interaction parameters after
[ atomtypes ] section as follows:

 [ nonbond_params ]
; i    j func          sigma      epsilon
CT    CT  1	       3.80000e-01  2.09200e-01

When I run grompp, the program complains that atom type CT is not found.
If I change CT to opls_182, then it works fine. However, when I check
oplsaabon.itp, CT is used, but not opls_182. Could anyone tell me why I
can't use atom type in *nb.itp? How can I fix it? If opls_182 is defined
as atom type, then how does gromacs recognize CT is **bon.itp?

By the way, my question relates to my previous question. Unfortunately,
no one answered it. I really appreciate someone can help me. The
following is my previous email:

In ffoplsaanb.itp, there are 8 columns.
; name  bond_type    mass    charge   ptype          sigma      epsilon
 opls_001   C   6      12.01100     0.500       A    3.75000e-01
4.39320e-01 ; SIG

In ffG53a5nb.itp, there are 7 columns.
[ atomtypes ]
;name  at.num   mass      charge ptype       c6           c12
    O    8      0.000      0.000     A  0.0022619536       1e-06

Could anyone tell me how gromacs knows to read 8 columns for oplsaa FF,
but 7 columns for gromos FF? Thanks!

All the best!


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