<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">From bond lengths, center of mass for the group and the moment of inertia.<div><br></div><div>Erik</div><div><br><div><div>27 mar 2012 kl. 14.54 skrev Song Ke:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>Dear All,<br><br>I have a question about create and simulate dopc lipid virtual sites. I<br>noticed in ffbonded.itp<br><br>[ constrainttypes ]<br>; this section is implemented manually from bond & angle values<br><br>; constraints for rigid CH3 groups<br> MCH3 CT 2 0.166426<br> MCH3 S 2 0.193875<br> MCH3 MCH3 2 0.092163<br>; constraints for rigid NH3 groups<br> MNH3 CT 2 0.158254<br> MNH3 MNH3 2 0.080229<br><br>; angle-derived constraints for OH and SH groups in proteins<br>; The constraint A-C is calculated from the angle A-B-C and bonds A-B, B-C.<br> C HO 2 0.195074<br> CA HO 2 0.195074<br> CT HO 2 0.194132<br> CT HS 2 0.235935<br><br><br>However, there is no MCH3 N constraint types, how can I get this value?<br><br>Meanwhile, Is there a website or scripts to generate the dopc virtual<br>sites bonded itp instead of do it manually?<br><br>Many thanks in advance,<br><br><br>-- <br>Song KE<br>PhD Candidate<br>Mailto:song.ke@univie.ac.at<br>Molecular Modeling Lab<br>Department of Pharmacology and Toxicology<br>University of Vienna<br>Althanstrasse 14 (UZA 2)<br>A-1090 Vienna, Austria<br><br>-- <br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!<br>Please don't post (un)subscribe requests to the list. Use the <br>www interface or send it to gmx-users-request@gromacs.org.<br>Can't post? Read http://www.gromacs.org/Support/Mailing_Lists<br></div></blockquote></div><br><div>
<span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div>-----------------------------------------------</div><div>Erik Marklund, PhD</div><div>Dept. of Cell and Molecular Biology, Uppsala University.</div><div>Husargatan 3, Box 596, 75124 Uppsala, Sweden</div><div>phone: +46 18 471 6688 fax: +46 18 511 755</div><div><a href="mailto:erikm@xray.bmc.uu.se">erikm@xray.bmc.uu.se</a></div><div><a href="http://www2.icm.uu.se/molbio/elflab/index.html">http://www2.icm.uu.se/molbio/elflab/index.html</a></div></div></span></div></span></span>
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