<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><div>Sorry for the subject in my last post.</div><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><br><div>Vidarebefordrat brev:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;"><span style="font-family:'Helvetica'; font-size:medium; color:rgba(0, 0, 0, 1);"><b>Från: </b></span><span style="font-family:'Helvetica'; font-size:medium;">Pär Bjelkmar <<a href="mailto:bjelkmar@cbr.su.se">bjelkmar@cbr.su.se</a>><br></span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;"><span style="font-family:'Helvetica'; font-size:medium; color:rgba(0, 0, 0, 1);"><b>Datum: </b></span><span style="font-family:'Helvetica'; font-size:medium;">25 augusti 2010 14.32.23 CEST<br></span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;"><span style="font-family:'Helvetica'; font-size:medium; color:rgba(0, 0, 0, 1);"><b>Till: </b></span><span style="font-family:'Helvetica'; font-size:medium;"><a href="mailto:gmx-developers@gromacs.org">gmx-developers@gromacs.org</a><br></span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;"><span style="font-family:'Helvetica'; font-size:medium; color:rgba(0, 0, 0, 1);"><b>Ämne: </b></span><span style="font-family:'Helvetica'; font-size:medium;"><b>Re: gmx-developers Digest, Vol 76, Issue 15</b><br></span></div><br><div>Hi,<br><br>It's something similar to what CHARMM does. They use a lot of such special linkages to combine existing "residues" into new ones, all protonation states for example but also some much more complicated things like "building" the DPPC lipid from Palmitate (PALM) and "PCGL", using two linkages (EST1 and EST2), called patches in CHARMM. <br><br>And this is also, I guess(?), why you, Roland, used the trick with the modified psfgen program (NAMD/VMD software) to build GROMACS topologies of your lignin and cellulose molecules: it could build the molecules modularly using the patches.<br><br>Regarding the CHARMM port: this modularity is why it's kind-of hard to port the CHARMM ff "completely".<br><br>/Pär Bjelkmar<br><br><blockquote type="cite">Message: 1<br></blockquote><blockquote type="cite">Date: Tue, 24 Aug 2010 19:44:07 -0400<br></blockquote><blockquote type="cite">From: Roland Schulz <<a href="mailto:roland@utk.edu">roland@utk.edu</a>><br></blockquote><blockquote type="cite">Subject: [gmx-developers] using replace/delete syntax of termini<br></blockquote><blockquote type="cite"><span class="Apple-tab-span" style="white-space:pre"> </span>database<span class="Apple-tab-span" style="white-space:pre"> </span>for specbond<br></blockquote><blockquote type="cite">To: Discussion list for GROMACS development<br></blockquote><blockquote type="cite"><span class="Apple-tab-span" style="white-space:pre"> </span><<a href="mailto:gmx-developers@gromacs.org">gmx-developers@gromacs.org</a>><br></blockquote><blockquote type="cite">Message-ID:<br></blockquote><blockquote type="cite"><span class="Apple-tab-span" style="white-space:pre"> </span><<a href="mailto:AANLkTim5=wX060wcv29XxuApPXdhEK8DLYnxg9dn23a_@mail.gmail.com">AANLkTim5=wX060wcv29XxuApPXdhEK8DLYnxg9dn23a_@mail.gmail.com</a>><br></blockquote><blockquote type="cite">Content-Type: text/plain; charset="iso-8859-1"<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Hi,<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">it would be very nice if it would be possible to use the replace/delete/add<br></blockquote><blockquote type="cite">features of the termini (tdb) files also in combination with specbond. This<br></blockquote><blockquote type="cite">would make it simpler to specify some non-standard linkages.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">As an example: Instead of fully specifying the CYS2 it would be nice to be<br></blockquote><blockquote type="cite">able to say:<br></blockquote><blockquote type="cite">[ CYS2 ]<br></blockquote><blockquote type="cite">[ replace ]<br></blockquote><blockquote type="cite"> CB opls_214 12.011 0.0975<br></blockquote><blockquote type="cite"> SG opls_203 32.06500 -0.2175<br></blockquote><blockquote type="cite">[ delete ]<br></blockquote><blockquote type="cite"> HG<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">For this example the saving would be very limited. But with a large number<br></blockquote><blockquote type="cite">of possible linkages this would give a considerable saving in specifying the<br></blockquote><blockquote type="cite">topology for possible combinations of linkages. The residue used as basis<br></blockquote><blockquote type="cite">(CYS) for the modified residue (CYS2) could come from the beginning of the<br></blockquote><blockquote type="cite">name or could be specified explicitly. This modified residue could be used<br></blockquote><blockquote type="cite">by a specbond line (which wouldn't change from the current line using<br></blockquote><blockquote type="cite">CYS2). It seems this feature could be implemented by a very limited patch<br></blockquote><blockquote type="cite">because it would use only features already implemented for termini. But I<br></blockquote><blockquote type="cite">don't understand the termini code so I can't judge this myself. Also I'm not<br></blockquote><blockquote type="cite">sure whether it might be a problem with the charge groups.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Would this be something easy and useful to add to pdb2gmx?<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Roland<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">-- <br></blockquote><blockquote type="cite">ORNL/UT Center for Molecular Biophysics <a href="http://cmb.ornl.gov/">cmb.ornl.gov</a><br></blockquote><blockquote type="cite">865-241-1537, ORNL PO BOX 2008 MS6309<br></blockquote><blockquote type="cite">-------------- next part --------------<br></blockquote><blockquote type="cite">An HTML attachment was scrubbed...<br></blockquote><blockquote type="cite">URL: <a href="http://lists.gromacs.org/pipermail/gmx-developers/attachments/20100824/e1017c7b/attachment-0001.html">http://lists.gromacs.org/pipermail/gmx-developers/attachments/20100824/e1017c7b/attachment-0001.html</a><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">------------------------------<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">-- <br></blockquote><blockquote type="cite">gmx-developers mailing list<br></blockquote><blockquote type="cite"><a href="mailto:gmx-developers@gromacs.org">gmx-developers@gromacs.org</a><br></blockquote><blockquote type="cite"><a href="http://lists.gromacs.org/mailman/listinfo/gmx-developers">http://lists.gromacs.org/mailman/listinfo/gmx-developers</a><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">End of gmx-developers Digest, Vol 76, Issue 15<br></blockquote><blockquote type="cite">**********************************************<br></blockquote><br></div></blockquote></div><br></div></div><br></body></html>