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
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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