<html><body><div style="color:#000; background-color:#fff; font-family:times new roman, new york, times, serif;font-size:12pt"><div><span>Dear Users,</span></div><div><br><span></span></div><div>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?<br></div><div>It seems that there are evidences that ARG residue remains protonated inside the membrane (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2275699/).</div><div>How about the HIS, LYS etc?<br></div><div><br></div><div>Sorry if it's a dull question, however I found very little comments on the subject.<br></div><div><br></div><div>Thanks in advance,</div><div><br></div><div>Ricardo.<br></div><div><font size="1"><i></i></font><font size="1"><i></i></font><div style="font-family: times new roman,new york,times,serif; font-size: 14pt;"><style><!--filtered {font-family:"Cambria Math";panose-1:2 4 5 3 5 4 6 3 2 4;}filtered
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