[gmx-users] OPLS-ff topology file for modified residue procedure?

[Neena Susan Eappen]

Hello gromacs users,

For MD simulations of a peptide in vacuum, I want to find OPLS force field compatible parameters for modified alanine residue in the peptide (with the carbonyl oxygen protonated .i.e. enol tautomer of peptide bond). Such a protonation site is possible in gas phase.

I was wondering do I use the mktop program suggested by gromacs to generate dihedrals, partial charges? Or use DFT for parameterization?

Thank you,
Neena
________________________________
From: Neena Susan Eappen
Sent: Tuesday, June 18, 2019 11:35 AM
To: gromacs.org_gmx-users at maillist.sys.kth.se
Subject: [gmx-users] OPLS-ff topology file for modified residue procedure?

Hello gromacs users,

For MD simulations of a peptide in vacuum, I want to find OPLS force field compatible parameters for modified alanine residue in the peptide (with the carbonyl oxygen protonated .i.e. enol tautomer of peptide bond). Such a protonation site is possible in gas phase.

I was wondering do I use the mktop program suggested by gromacs to generate it?

Thank you,
Neena