One additional thing would need to be changed for my proposal to work for polymers with different linkages.<div><br></div><div>If I'm not mistaken, specbond is currently applied the following way: </div><div><br></div>
<div>As an example consider a residue X which has two linkages and thus 2 rules apply. Let's assume the first rule would rename X to X1 and the 2nd rule would rename X to XA. Even if the first rule is applied before the 2nd rule then the 2nd rule still has to refer to X/X1 as X and not X1. Thus columns 1 and 4 always refer to the residue with its originally name given in the pdb file and not by its new name given by a prior rule. </div>
<div><br></div><div>This behavior makes it impossible to rename a residue consecutive based on two rules. Being able to rename in two steps would allow to use specbonds in cases like lignin with different possible linkages. One could use one specbond rule to rename X to X1 or X2 depending of the preceding linkage "1" or "2" in the chain and then to X1A, X1B, X2A or X2B depending on the following linkage A or B. </div>
<div><br></div><div>Thus we would need to either:</div><div>- Change the behavior that specbond uses the prior renamed residue name for a following rule for columns 1-4, or</div><div>- Have additional columns which would allow to specify the name of a residue based on the prior changed name of an earlier rule</div>
<div><br></div><div> Roland</div><div><br><div class="gmail_quote">On Wed, Aug 25, 2010 at 12:17 PM, Roland Schulz <span dir="ltr"><<a href="mailto:roland@utk.edu">roland@utk.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<br><br><div class="gmail_quote"><div class="im">On Wed, Aug 25, 2010 at 10:18 AM, Pär Bjelkmar <span dir="ltr"><<a href="mailto:bjelkmar@cbr.su.se" target="_blank">bjelkmar@cbr.su.se</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div style="word-wrap:break-word"><div><div style="word-wrap:break-word"><div><blockquote type="cite"><div style="margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0px"><br></div><div>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>
</div></blockquote></div></div></div></div></blockquote></div><div>Yes. It is similar to the CHARMM patches. But I tried to modify how patches work within CHARMM to a a format which matches the current syntax of terminal databases and specbond, with the hope to make it easy to implement. </div>
<div class="im">
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word"><div><div style="word-wrap:break-word"><div><blockquote type="cite"><div>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>
</div></blockquote></div></div></div></div></blockquote></div><div> Yes. While cellulose is easy to describe with GROMACS topogies lignin is more difficult. Lignin has 4 different linkages and can be branched. Thus a residue can be modified at 2 or 3 sites by either one of the 4 linkages. Thus the monomer can be modified in 4^3+4^2 different ways (a few less because some are exclusive but other linkages also exist). Generating those ~80 versions of a monomer by hand is of course not very nice. Thus we decided to use the modified psfgen. Now we would like to try virtual sites with lignin and thus we look at this issue again.</div>
<div class="im">
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word"><div><div style="word-wrap:break-word"><div><blockquote type="cite"><div>Regarding the CHARMM port: this modularity is why it's kind-of hard to port the CHARMM ff "completely".<br>
</div></blockquote></div></div></div></div></blockquote></div><div>Would my proposed extension (using the tdb syntax similar to patches) help with porting the parts of the CHARMM ff which remains to be ported?</div><div>
<br></div><font color="#888888">
<div>Roland</div></font><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div></div><div class="h5"><div style="word-wrap:break-word"><div><div style="word-wrap:break-word">
<div><blockquote type="cite">
<div><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" target="_blank">roland@utk.edu</a>><br>
</blockquote><blockquote type="cite">Subject: [gmx-developers] using replace/delete syntax of termini<br></blockquote><blockquote type="cite"><span style="white-space:pre-wrap"> </span>database<span style="white-space:pre-wrap"> </span>for specbond<br>
</blockquote><div><blockquote type="cite">To: Discussion list for GROMACS development<br></blockquote><blockquote type="cite"><span style="white-space:pre-wrap"> </span><<a href="mailto:gmx-developers@gromacs.org" target="_blank">gmx-developers@gromacs.org</a>><br>
</blockquote></div><blockquote type="cite">Message-ID:<br></blockquote><blockquote type="cite"><span style="white-space:pre-wrap"> </span><<a href="mailto:AANLkTim5=wX060wcv29XxuApPXdhEK8DLYnxg9dn23a_@mail.gmail.com" target="_blank">AANLkTim5=wX060wcv29XxuApPXdhEK8DLYnxg9dn23a_@mail.gmail.com</a>><br>
</blockquote><blockquote type="cite">Content-Type: text/plain; charset="iso-8859-1"<br></blockquote><div><div></div><div><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>
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