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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