I was trying to make the OPLS-AA topology file for single amino acid residue (zwitter form of Phenylalanine) using pdb2gmx. I found that the output topology created includes charges different as mentioned in this paper “https://pubs.acs.org/doi/pdf/10.1021/ja00214a001”.
So should I correct the charges as per the paper. So Pdb2gmx does not give us the correct topology file when used for aminoacids, peptides or proteins ?
OPLS-AA force field implemented in GROMACS is based on the publications below
; This force field uses a format that requires Gromacs 3.1.4 or later.
; References for the OPLS-AA force field:
; W. L. Jorgensen, D. S. Maxwell, and J. Tirado-Rives,
; J. Am. Chem. Soc. 118, 11225-11236 (1996).
; W. L. Jorgensen and N. A. McDonald, Theochem 424, 145-155 (1998).
; W. L. Jorgensen and N. A. McDonald, J. Phys. Chem. B 102, 8049-8059 (1998).
; R. C. Rizzo and W. L. Jorgensen, J. Am. Chem. Soc. 121, 4827-4836 (1999).
; M. L. Price, D. Ostrovsky, and W. L. Jorgensen, J. Comp. Chem. (2001).
; E. K. Watkins and W. L. Jorgensen, J. Phys. Chem. A 105, 4118-4125 (2001).
; G. A. Kaminski, R.A. Friesner, J.Tirado-Rives and W.L. Jorgensen, J. Phys. Chem. B 105, 6474 (2001).
The parameters you plan to use come from a previous paper (JACS, 1988). It can be that charge distributions are different among two force field versions.