[gmx-users] Peptide protonation inside membrane

Ricardo O. S. Soares ross_usp at yahoo.com.br
Thu Feb 23 21:40:23 CET 2012

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.

Thanks in advance,

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