With regards to topic 2. Back calculation of RDC (Prem Prakash Pathak) Dear Prem,
As far as I know this is not possible with Xplor(-NIH). Unless you introduce an artificial alignment tensor (knowing the orientation in advance). This is complicated in ,my opinion. Another way to do so, is with PALES from Zweckstetter (Link:) http://www.mpibpc.mpg.de/groups/griesinger/zweckstetter/_linkssoftware_pales.htm (one line in adress bar of internet browser) Or using a matlab script designed in our group by Bin Wu. (I can send a reference later, if you like) I reprogrammed this into a python script. Sorry I cannot give you the reference now. I just arrived at home, and dinner is cooling down as I type. Kind regards, Ramon van der Werf > 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. Small-molecule generation for X-plor-NIH (Keith L Constantine) > 2. Back calculation of RDC (Prem Prakash Pathak) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 07 Jul 2008 09:07:03 -0400 > From: Keith L Constantine <keith.constantine at bms.com> > Subject: [Xplor-nih] Small-molecule generation for X-plor-NIH > To: xplor-nih at nmr.cit.nih.gov > Message-ID: <487214F7.7070708 at bms.com> > Content-Type: text/plain; charset="iso-8859-1" > > 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 > -------------- 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/20080707/0b08816f/attachment-0001.vcf > > ------------------------------ > > Message: 2 > Date: Mon, 7 Jul 2008 18:56:21 +0530 > From: "Prem Prakash Pathak" <prempolymer at gmail.com> > Subject: [Xplor-nih] Back calculation of RDC > To: Xplor-nih at nmr.cit.nih.gov > Message-ID: > <e03676150807070626w129419ccm88c4a894a832d6e7 at mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > Dear Users, > > is it possible to calculate residual dipoar coupling parameters > theoretically given only a PDB structure of protein and no > experimental parameters. > > regards > > Prem > > > ------------------------------ > > _______________________________________________ > 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 1 > **************************************** >
