<html><body><div style="color:#000; background-color:#fff; font-family:times new roman, new york, times, serif;font-size:12pt"><div><span>Dear All,</span></div><div><span></span> </div><div><span>For pdb2gmx, we have -ignh. Does -ignh will always give the correct HIS format at pH 7?</span></div><div><span></span> </div><div><span>Looking forward to getting your reply.</span></div><div><span></span> </div><div><span>Cheers,</span></div><div><span></span> </div><div><span>Acoot</span></div><div><br></div> <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 size="2" face="Arial"> <div style="margin: 5px 0px; padding: 0px; border: 1px solid rgb(204, 204, 204); height: 0px; line-height: 0; font-size: 0px;" class="hr" contentEditable="false" readonly="true"></div> <b><span style="font-weight:
bold;">From:</span></b> lina <lina.lastname@gmail.com><br> <b><span style="font-weight: bold;">To:</span></b> Acoot Brett <acootbrett@yahoo.com>; Discussion list for GROMACS users <gmx-users@gromacs.org> <br> <b><span style="font-weight: bold;">Sent:</span></b> Thursday, 5 April 2012 10:55 PM<br> <b><span style="font-weight: bold;">Subject:</span></b> Re: [gmx-users] the different protonation state of HIS<br> </font> </div> <br>On Thu, Apr 5, 2012 at 7:14 PM, Acoot Brett <<a href="mailto:acootbrett@yahoo.com" ymailto="mailto:acootbrett@yahoo.com">acootbrett@yahoo.com</a>> wrote:<br>> Dear All,<br>><br>> For the different protonation state of HIS, what are there 3-letter code for<br>> GROMACS? And how about -SH and -S-S- codon? Or do you have a web link for me<br>> to read? Do we still have any other confusing amino acids?<br><br>In pdb2gmx -his<br><br>you will get something like below<br><br>0. H on ND1 only
(HSD)<br>1. H on NE2 only (HSE)<br>2. H on ND1 and NE2 (HSP)<br>3. Coupled to Heme (HIS1)<br><br>Then based on the pka value and the PH, you can make a choice.<br><br>><br>> I am looking forward to getting a reply from you.<br>><br>> Cheers,<br>><br>> Acoot<br>><br>> --<br>> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" ymailto="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>> <a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>> Please search the archive at<br>> <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>> Please don't post (un)subscribe requests to the list. Use the<br>> www interface or send it to <a href="mailto:gmx-users-request@gromacs.org"
ymailto="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>> Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br><br><br> </div> </div> </div></body></html>