[gmx-users] oplsaa force field
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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