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
