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
>
>
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