<HTML><BODY style="word-wrap: break-word; -khtml-nbsp-mode: space; -khtml-line-break: after-white-space; ">Hi Erik,<DIV><BR class="khtml-block-placeholder"></DIV><DIV>Right. I see your point. I was actually considering making vsite construction of hydrogens fully automatic, since there is virtually no geometrical data for them in refi_aa.dat, and one will have to rely on the force field for their angles etc anyway. Also, as you suggest, it would reduce the size of the vsite data file by a fair amount. I would however, paranoid as I am, stay away from the input structure and rely on the force field for vsite generation.</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>For the more complicated groups, such as aromatics, It would be nice to have one generic data file instead of one for each force field as is the case now. It doesn't really comply with the 'mimic the ff' idea, but makes it much easier to maintain the vsite data. Then the question is whether one really need anything more than what's in the current ddb files: angles and bond lengths, that is. All such groups are planar anyway, so no VStype has to be provided to the program. Masses will always have to be generated, and planarity/symmetry will be redundant/irrelevant information.</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>I will give this some more thought.</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>Thanks for the input.</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>/Erik</DIV><BR><DIV><DIV>1 okt 2007 kl. 12.34 skrev Erik Lindahl:</DIV><BR class="Apple-interchange-newline"><BLOCKQUOTE type="cite">Hi Erik,<DIV><BR class="khtml-block-placeholder"></DIV><DIV>David and I spoke about this last friday, and I'm not sure I agree completely :-)</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>First, this approach is just moving the problem. Instead of having to create dummy settings for each force field you end up having to specify dummy parameters for each new molecule/residue. This will really be a pain for people working with small organic compounds, etc.</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>The current aromatic vsites are horrible (construction-wise, I'm not even thinking about their usefullness...) and should be replaced, but the "standard" hydrogen vsites can actually be constructed completely automatic for new molecules.</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>I've looked at quite a few vsites manually the last couple of days, and the largest deviations by far occur in peptide groups and similar constructs that aren't exactly planar in reality, but the vsite construction forces them to be. There's nothing we can do about that, and in comparison the deviations between ideal and force-field values e.g. for CH2 angles are very small.</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>The other problem concerns e.g. NH2 groups. If I recall correctly these are sometimes planar in Gromos96, while OPLS/Amber model them as non-planar. In my opinion the right thing to do in that case is to model the force field as good as possible, since the point is to remove degrees of freedom while altering as little as possible. Otherwise we should for consistency also alter the constraint lengths of all bonds to agree with experimental structures rather than the equilibrium values in the force field.</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>So, it's definitely worth cleaning up, it would be nice to generate the MC/MN dummy mass parameters automatically from the force field (easy), and then create a residue-specific database for "advanced" constructs such as virtual aromatic sidechains. I still think it's more correct to set the simple vsites from the force field, though, or possibly the input structure.</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>Cheers,</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>Erik</DIV><DIV><BR><DIV><DIV>On Oct 1, 2007, at 11:03 AM, Erik Marklund wrote:</DIV><BR class="Apple-interchange-newline"><BLOCKQUOTE type="cite">Hi,<DIV><BR class="khtml-block-placeholder"></DIV><DIV>I've put some text on the wiki for genvsites (<A href="http://wiki.gromacs.org/index.php/Genvsites">http://wiki.gromacs.org/index.php/Genvsites</A>) describing the current state of things. We've decided to make a force field independent description of the virtual site constructions, which does not contain much geometrical nor topological information. Ideal geometries will be constructed from refi_aa.dat, containing crystallographic bond/angle/tortional data, from which in turn center of mass and moment of inertia will be calculated when needed. We're aiming to make the program 'stupid', i.e. not make too many assumptions or smart decisions, and just read and interpret the vsite data file. Some information will be taken from the topology, and perhaps also from the force field in special cases. Any comments on the proposed file format or the overall strategy is greatly appreciated.</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>Over and out.</DIV><DIV><BR><DIV> <SPAN class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><SPAN class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><SPAN class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><SPAN class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><BLOCKQUOTE type="cite"></BLOCKQUOTE><DIV>_______________________________________________</DIV><DIV>Erik Marklund, PhD student</DIV><DIV>Laboratory of Molecular Biophysics,</DIV><DIV>Dept. of Cell and Molecular Biology, Uppsala University.</DIV><DIV>Husargatan 3, Box 596,<SPAN class="Apple-tab-span" style="white-space:pre"><SPAN class="Apple-style-span" style="white-space: pre; "><SPAN class="Apple-style-span" style="white-space: pre; "><SPAN class="Apple-style-span" style="white-space: pre; "> </SPAN></SPAN></SPAN></SPAN>75124 Uppsala, Sweden</DIV><DIV>phone:<SPAN class="Apple-tab-span" style="white-space:pre"><SPAN class="Apple-style-span" style="white-space: pre; "><SPAN class="Apple-style-span" style="white-space: pre; "><SPAN class="Apple-style-span" style="white-space: pre; "> </SPAN></SPAN></SPAN></SPAN>+46 18 471 4537<SPAN class="Apple-tab-span" style="white-space:pre"><SPAN class="Apple-style-span" style="white-space: pre; "><SPAN class="Apple-style-span" style="white-space: pre; "><SPAN class="Apple-style-span" style="white-space: pre; "> </SPAN></SPAN></SPAN></SPAN>fax: +46 18 511 755</DIV><DIV><A href="mailto:erikm@xray.bmc.uu.se">erikm@xray.bmc.uu.se</A><SPAN class="Apple-tab-span" style="white-space:pre"><SPAN class="Apple-style-span" style="white-space: pre; "><SPAN class="Apple-style-span" style="white-space: pre; "><SPAN class="Apple-style-span" style="white-space: pre; "> </SPAN></SPAN></SPAN></SPAN><A href="http://xray.bmc.uu.se/molbiophys">http://xray.bmc.uu.se/molbiophys</A></DIV><BR class="Apple-interchange-newline"></SPAN></SPAN></SPAN></SPAN> </DIV><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">_______________________________________________</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">gmx-developers mailing list</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><A href="mailto:gmx-developers@gromacs.org">gmx-developers@gromacs.org</A></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><A href="http://www.gromacs.org/mailman/listinfo/gmx-developers">http://www.gromacs.org/mailman/listinfo/gmx-developers</A></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Please don't post (un)subscribe requests to the list. Use the<SPAN class="Apple-converted-space"> </SPAN></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">www interface or send it to <A href="mailto:gmx-developers-request@gromacs.org">gmx-developers-request@gromacs.org</A>.</DIV> </BLOCKQUOTE></DIV><BR></DIV></BLOCKQUOTE></DIV><BR><DIV> <SPAN class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><SPAN class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><SPAN class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><SPAN class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><BLOCKQUOTE type="cite"></BLOCKQUOTE><DIV>_______________________________________________</DIV><DIV>Erik Marklund, PhD student</DIV><DIV>Laboratory of Molecular Biophysics,</DIV><DIV>Dept. of Cell and Molecular Biology, Uppsala University.</DIV><DIV>Husargatan 3, Box 596,<SPAN class="Apple-tab-span" style="white-space:pre"><SPAN class="Apple-style-span" style="white-space: pre; "><SPAN class="Apple-style-span" style="white-space: pre; "><SPAN class="Apple-style-span" style="white-space: pre; "> </SPAN></SPAN></SPAN></SPAN>75124 Uppsala, Sweden</DIV><DIV>phone:<SPAN class="Apple-tab-span" style="white-space:pre"><SPAN class="Apple-style-span" style="white-space: pre; "><SPAN class="Apple-style-span" style="white-space: pre; "><SPAN class="Apple-style-span" style="white-space: pre; "> </SPAN></SPAN></SPAN></SPAN>+46 18 471 4537<SPAN class="Apple-tab-span" style="white-space:pre"><SPAN class="Apple-style-span" style="white-space: pre; "><SPAN class="Apple-style-span" style="white-space: pre; "><SPAN class="Apple-style-span" style="white-space: pre; "> </SPAN></SPAN></SPAN></SPAN>fax: +46 18 511 755</DIV><DIV><A href="mailto:erikm@xray.bmc.uu.se">erikm@xray.bmc.uu.se</A><SPAN class="Apple-tab-span" style="white-space:pre"><SPAN class="Apple-style-span" style="white-space: pre; "><SPAN class="Apple-style-span" style="white-space: pre; "><SPAN class="Apple-style-span" style="white-space: pre; "> </SPAN></SPAN></SPAN></SPAN>http://xray.bmc.uu.se/molbiophys</DIV><BR class="Apple-interchange-newline"></SPAN></SPAN></SPAN></SPAN> </DIV><BR></BODY></HTML>