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
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