<html><body><div style="color:#000; background-color:#fff; font-family:times new roman, new york, times, serif;font-size:12pt"><div><span>Hi Justin,</span></div><div><span>thanks, for your reply.</span></div><div><span>I'm going to check H++ tools on my system.</span></div><div><br><span></span></div><div><span>Cheers,<br></span></div><div> </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 {font-family:Calibri;panose-1:2 15 5 2 2 2 4 3 2 4;}p.MsoNormal, li.MsoNormal, div.MsoNormal {margin-top:0cm;margin-right:0cm;margin-bottom:10.0pt;margin-left:0cm;line-height:115%;font-size:11.0pt;font-family:"sans-serif";}a:link, span.MsoHyperlink {color:blue;text-decoration:underline;}a:visited, span.MsoHyperlinkFollowed {color:purple;text-decoration:underline;}.MsoChpDefault
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<font size="1"> </font></span></div><font size="1">Ricardo O. S. Soares , PhD Student.<br>Group of Biological Physics - Department of Physics & Chemistry<br>Faculty of Pharmaceutical Sciences at Ribeirão Preto - University of São Paulo.<br></font><br></div></div><div><br><blockquote style="border-left: 2px solid rgb(16, 16, 255); margin-left: 5px; margin-top: 5px; padding-left: 5px;"> <div style="font-family: times new roman, new york, times, serif; font-size: 12pt;"> <div style="font-family: times new roman, new york, times, serif; font-size: 12pt;"> <div dir="ltr"> <font face="Arial" size="2"> <hr size="1"> <b><span style="font-weight:bold;">De:</span></b> Justin A. Lemkul <jalemkul@vt.edu><br> <b><span style="font-weight: bold;">Para:</span></b> Ricardo O. S. Soares <ross_usp@yahoo.com.br>; Discussion list for GROMACS users <gmx-users@gromacs.org> <br> <b><span style="font-weight: bold;">Enviadas:</span></b>
Quinta-feira, 23 de Fevereiro de 2012 18:07<br> <b><span style="font-weight: bold;">Assunto:</span></b> Re: [gmx-users] Peptide protonation inside membrane<br> </font> </div> <br><br><br>Ricardo O. S. Soares wrote:<br>> Dear Users,<br>> <br>> 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>> It seems that there are evidences that ARG residue remains protonated inside the membrane (<a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2275699/" target="_blank">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2275699/</a>).<br>> How about the HIS, LYS etc?<br>> <br>> Sorry if it's a dull question, however I found very little comments on the subject.<br>> <br><br>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:<br><br><a href="http://biophysics.cs.vt.edu/" target="_blank">http://biophysics.cs.vt.edu/</a><br><br>-Justin<br><br>-- ========================================<br><br>Justin A. Lemkul<br>Ph.D. Candidate<br>ICTAS Doctoral Scholar<br>MILES-IGERT Trainee<br>Department of Biochemistry<br>Virginia Tech<br>Blacksburg, VA<br>jalemkul[at]vt.edu | (540) 231-9080<br><a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br><br>========================================<br><br><br> </div> </div> </blockquote></div> </div></body></html>