Hi folks, please be aware that the CNS topology and parameter files created by PRODRG only contain polar hydrogens, although the PDB files they create contain all the hydrogens. To quote from their FAQ:
Q: I get a PDB file with all hydrogens but the topology files only contain information for hydrogens attached to non-carbon atoms? A: That's right. PRODRG is intimately linked in with the concept of "united-atoms" which is used in many force fields to (drastically) reduce the total number of atoms. This is unlikely to change in the near future and indeed therefore makes PRODRG topologies unsuitable for use with NMR-type calculations or all-atom force fields. So for NMR Xplor users you still have to edit the CNS files from PRODRG and most importantly add the hydrogens yourself. But it is useful for helping to iron out errors with impropers for weird residues. cheers, Martin On 12/07/2008, at 2:00 AM, xplor-nih-request at nmr.cit.nih.gov wrote: > Send Xplor-nih mailing list submissions to > xplor-nih at nmr.cit.nih.gov > > To subscribe or unsubscribe via the World Wide Web, visit > http://dcb.cit.nih.gov/mailman/listinfo/xplor-nih > or, via email, send a message with subject or body 'help' to > xplor-nih-request at nmr.cit.nih.gov > > You can reach the person managing the list at > xplor-nih-owner at nmr.cit.nih.gov > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Xplor-nih digest..." > > > Today's Topics: > > 1. Re: Small-molecule generation for X-plor-NIH (Keith L > Constantine) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 11 Jul 2008 11:21:07 -0400 > From: Keith L Constantine <keith.constantine at bms.com> > Subject: Re: [Xplor-nih] Small-molecule generation for X-plor-NIH > To: John Kuszewski <johnk at mail.nih.gov> > Cc: "Metzler, William J" <william.metzler at bms.com>, > xplor-nih at nmr.cit.nih.gov, Mueller Luciano <luciano.mueller at > bms.com> > Message-ID: <48777A63.4000101 at bms.com> > Content-Type: text/plain; charset="iso-8859-1" > > Hi John: > > Thanks a lot for the update. Guillermo Bermejo sent me a message > (partially reproduced below) about a server for small molecule file > generation. For us, server securuity is always an issue. > > As I mentioned, the facilites that at one time were available in > Quanta > were quite convenient for generating small molecule files for X-plor. > Please let me know if you become aware of any current software that > does > this, or if this type of utitlity is incorporated at some point > into the > xplor-NIH GUI. > > Thanks again, > > Keith > > > ...on the Xplor-NIH FAQ page: (http://nmr.cit.nih.gov/xplor-nih/ > faq.html) (FAQ #2). There they redirect the reader to the Dundee > PRODRG2 Server (http://davapc1.bioch.dundee.ac.uk/programs/ > prodrg/). I'm not sure this is exactly what you want (more user > frindly, currently supported, ..., than what you are using), but I > recently used it for the first time and found it helpful. In brief, > you upload a text file to the server containing the "formula" of > the molecule; for example citrate looks like (example provided in > the server webpage): > > O O > | | > O=C O C=O > | | | > C-C-C > | > C=O > | > O > > Given the "fomula" the server provides a paramter, a topology, and > a pdb file. The only catch is that the files are for CNS, but they > are easy to convert to Xplor. I hope this helps. > > > > John Kuszewski wrote: > >> Hi Keith, >> >> Sorry, but none of that functionality is available in the xplor-NIH >> GUI (aka VMD-xplor). It handles visualizing things reasonably well, >> and can show NOE, RDC, and Jcoupling violations and so forth, but no >> small-molecule topology/parameter generation. Charles and I have >> talked about ways to handle that sort of thing (usually starting from >> a PDB of a small molecule), but it's still just talk--no code. We >> know this is of great interest to y'all in the real world, but it's a >> non-trivial problem, as I'm sure you realize. >> >> --JK >> >> On Jul 7, 2008, at 9:07 AM, Keith L Constantine wrote: >> >>> All: >>> >>> We have in the past used a (no longer supported) version of the >>> program Quanta to generate the files needed for small organic >>> molecules for NMR structure determinations using XPLOR (or XPLOR- >>> NIH) with small molecules bound to proteins. >>> >>> Briefly, one could read a small molecule (MyMolecule.mol), >>> visualize >>> the molecule, change bond orders, change atom types, change atom >>> names, delete atoms, etc., and minimize the molecule in the CHARMM >>> force field. One could then enter the "NMR" file menues in the old >>> version of QUANTA and generate parameter (MyMolecule.xprm), >>> structure (MyMolecule.xpsf) and pdb (MyMolecule.pdb) files for the >>> small molecule, which could then be used in XPLOR. >>> >>> Does anyone know if there are any currently supported graphical >>> packages that can be used to perform the tasks described above? Are >>> any of these features available in the XPLOR-NIH GUI? >>> >>> Any help on this would be greatly appreciate. >>> >>> Keith >>> Constantine<keith.constantine.vcf>__________________________________ >>> __ >>> ___________ >>> Xplor-nih mailing list >>> Xplor-nih at nmr.cit.nih.gov >>> http://dcb.cit.nih.gov/mailman/listinfo/xplor-nih >> >> > -------------- next part -------------- > A non-text attachment was scrubbed... > Name: keith.constantine.vcf > Type: text/x-vcard > Size: 425 bytes > Desc: not available > Url : http://dcb.cit.nih.gov/pipermail/xplor-nih/attachments/ > 20080711/ead961d9/attachment-0001.vcf > > ------------------------------ > > _______________________________________________ > Xplor-nih mailing list > Xplor-nih at nmr.cit.nih.gov > http://dcb.cit.nih.gov/mailman/listinfo/xplor-nih > > > End of Xplor-nih Digest, Vol 65, Issue 4 > ****************************************
