With regards to calculation of RDCs without any known parameters except structure.
For completeness I send the reference which I mentioned in my previous posting: Wu, B.; Petersen, M.; Girard, F.; Tessari, M.; Wijmenga, S.S. (2006): J.Biomol. NMR., 35,103-115 This article decribes a method to calculate both alignment tensor and RDCs based on electrostatical parameters together with the gyration tensor. Regards, Ramon On Tue, 2008-07-08 at 12:00 -0400, 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: Xplor-nih Digest, Vol 65, Issue 1 (R.vanderWerf at nmr.ru.nl) > 2. Re: Small-molecule generation for X-plor-NIH (John Kuszewski) > 3. Re: Back calculation of RDC (Charles at Schwieters.org) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 7 Jul 2008 18:30:16 +0200 (CEST) > From: R.vanderWerf at nmr.ru.nl > Subject: Re: [Xplor-nih] Xplor-nih Digest, Vol 65, Issue 1 > To: xplor-nih at nmr.cit.nih.gov > Message-ID: > <40475.81.71.169.21.1215448216.squirrel at squirrel.science.ru.nl> > Content-Type: text/plain;charset=iso-8859-1 > > 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 > > **************************************** > > > > > > > ------------------------------ > > Message: 2 > Date: Mon, 7 Jul 2008 18:54:21 -0400 > From: John Kuszewski <johnk at mail.nih.gov> > Subject: Re: [Xplor-nih] Small-molecule generation for X-plor-NIH > To: Keith L Constantine <keith.constantine at bms.com> > Cc: xplor-nih at nmr.cit.nih.gov > Message-ID: <23159FB5-D961-4216-A9E0-83CB29319714 at mail.nih.gov> > Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed > > 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 > > > > ------------------------------ > > Message: 3 > Date: Mon, 07 Jul 2008 19:11:09 -0400 > From: Charles at Schwieters.org > Subject: Re: [Xplor-nih] Back calculation of RDC > To: "Prem Prakash Pathak" <prempolymer at gmail.com> > Cc: Xplor-nih at nmr.cit.nih.gov > Message-ID: <E1KFzrR-0001wS-EV at oaf.wireless> > > -----BEGIN PGP SIGNED MESSAGE----- > Hash: SHA1 > > > Hello Prem-- > > > > > is it possible to calculate residual dipoar coupling parameters > > theoretically given only a PDB structure of protein and no > > experimental parameters. > > > > Not at present: look at a program such as Pales for this functionality. > > best regards-- > Charles > -----BEGIN PGP SIGNATURE----- > Version: GnuPG v1.4.6 (GNU/Linux) > Comment: Processed by Mailcrypt 3.5.8+ <http://mailcrypt.sourceforge.net/> > > iD8DBQFIcqKNPK2zrJwS/lYRAkzaAJ41AgmPo0nTkigsryxZMCGIhRvVRgCbB51J > PyJfsUdTSD46OkqDFM8iSgs= > =xECy > -----END PGP SIGNATURE----- > > > ------------------------------ > > _______________________________________________ > 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 2 > **************************************** >
