[gmx-users] Converting protonated protein with pdb2gmx

[Deniz KARASU]

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?

Thanks.

Deniz.
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