[gmx-users] Protonation state of the ionisable residues

James Starlight jmsstarlight at gmail.com
Wed Feb 22 14:20:05 CET 2012

Thanks Justin.

Your aproach is very usefull indeed.

I've just one relative question about CAPPING of the termi in the case of
simulation of the membrane receptors. In that proteins both of N and C
termi are in the water polar layer. In the literature I've  found nothing
about capping of the termi as well as changing of protonated state of that
fragments. What advantages might have such capping of the termni of that


2012/2/22 Justin A. Lemkul <jalemkul at vt.edu>

> James Starlight wrote:
>> Dear Gromacs Users!
>> I'd like to change default protonation state of some specified Glu and
>> Asp residues im my protein.
>> By defaylt pdb2gmx -ignh create unprotonated state of the negatively
>> charged residues but I want to make 2 of such residues protonated to mimick
>> some intermollecular interactions.
>> How I could make such edition to my structure ? Is it possible to make
>> such changing AFTER pdb2gmx processing of my structure ( manually editiong
>> GRO or PDB file and TOPOLOGY)?
> It is possible, but would be an extreme hassle and would be very
> error-prone. You'd have to add in the new atoms, renumber *all* subsequent
> bonded and nonbonded interactions.
> The better approach is to re-create the topology with pdb2gmx -asp -glu.
> -Justin
> --
> ==============================**==========
> 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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
> ==============================**==========
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