[gmx-users] Peptide protonation inside membrane

Ricardo O. S. Soares ross_usp at yahoo.com.br
Fri Feb 24 07:12:09 CET 2012

Hi Justin,
thanks, for your reply.
I'm going to check H++ tools on my system.



 Ricardo O. S. Soares , PhD Student.
Group of Biological Physics - Department of Physics & Chemistry
Faculty of Pharmaceutical Sciences at Ribeirão Preto - University of São Paulo.

> De: Justin A. Lemkul <jalemkul at vt.edu>
>Para: Ricardo O. S. Soares <ross_usp at yahoo.com.br>; Discussion list for GROMACS users <gmx-users at gromacs.org> 
>Enviadas: Quinta-feira, 23 de Fevereiro de 2012 18:07
>Assunto: Re: [gmx-users] Peptide protonation inside membrane
>Ricardo O. S. Soares wrote:
>> Dear Users,
>> when using pdb2gmx with the -inter flag, how should one manage the residues charges of a peptide which is fully embedded in a lipid bilayer?
>> It seems that there are evidences that ARG residue remains protonated inside the membrane (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2275699/).
>> How about the HIS, LYS etc?
>> Sorry if it's a dull question, however I found very little comments on the subject.
>There is quite a lot in the literature about pKa shifting based on different microenvironments.  There are also a number of tools available to do pKa estimates, for instance:
>-- ========================================
>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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