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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