[gmx-users] Converting protonated protein with pdb2gmx

Justin A. Lemkul jalemkul at vt.edu
Fri Oct 29 21:05:29 CEST 2010

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.


> Thanks.
> Deniz. 


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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