Hi Justin, I am trying to simulate a peptide in vacuum and it has been shown that carbonyl oxygen is a favorable site of protonation in gas phase, hence I was looking for protonated carbonyl force field parameters.
Thank you, Neena ________________________________ From: Neena Susan Eappen Sent: Tuesday, April 16, 2019 7:21 PM To: [email protected] Subject: Re: [gmx-users] -ignh command removes protonation site of interest I am using OPLS-AA force field and there are no parameters for protonated carbonyl for alanine residue. How do I go about this? Thank you, Neena ________________________________ From: Neena Susan Eappen Sent: Monday, April 15, 2019 10:30 PM To: [email protected] Subject: [gmx-users] -ignh command removes protonation site of interest Hello gromacs users, I started with a peptide where protonation site was on a carbonyl oxygen. However, using -ignh command in pdb2gmx, I lose that proton from there. Any insights on how to move forward? Many thanks, Neena -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to [email protected].
