[gmx-users] Converting protonated protein with pdb2gmx

Deniz KARASU karasudeniz at gmail.com
Fri Oct 29 22:10:19 CEST 2010

Thanks Justin,

I think that I have to write a script to  remove hydrogens that are not
suitable for united-atom forcefield. After this operation I can use

On Fri, Oct 29, 2010 at 10:05 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

> 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
> 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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