[gmx-users] Protonation state of the ionisable residues

Justin A. Lemkul jalemkul at vt.edu
Wed Feb 22 13:34:18 CET 2012

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 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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