Deniz KARASU wrote:
Hi all,

I'm trying to convert a protein, that is protonated with another special software and by manually checking, with pdb2gmx. I am using FF53A6 forcefield and don't use -ignh option. When I run pdb2gmx it gives me this error.

Atom HA in residue VAL 1 not found in rtp entry with 8 atoms
             while sorting atoms. Maybe different protonation state.
             Remove this hydrogen or choose a different protonation state.
             Option -ignh will ignore all hydrogens in the input.

I understand that the hydrogen atom is not defined in forcefield for VAL residue and need selection protonation state interactively. I wonder that there is anyway to convert protonated protein for specified forcefield (including united-atom ff) and assign automatically protonation state according to bonded hydrogen in structure?


You can't choose to ignore some H atoms while recognizing others. Either you provide pdb2gmx with a suitable structure that can be used exactly by the force field, or you let pdb2gmx assign protonation states after ignoring all input H atoms. Fortunately, for all termini and titratable residues, you can do so with the -ter and -inter options.

-Justin

Thanks.

Deniz.

--
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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