[gmx-users] MCSS implemented?
spoel at xray.bmc.uu.se
Thu Aug 29 22:29:18 CEST 2002
On Thu, 2002-08-29 at 22:12, Paul Czodrowski wrote:
> Dear Gromacs Users,
> is there any possibility to perform a MCSS (multiple copy simultaneous
> search) calculation with Gromacs? This method was introduced by Karplus in
> order to calculate functionality maps for many different funtional
> In my simple understanding the binding pocket would be filled with a
> functional group (e.g. ammonia) and after running the MCSS procedure one
> could see a distribution of the particular functional group. You repeat
> thid procedure for different groups and create with this manner a map.
> Can you do this with Gromacs (I didn't find it...)?
There is nothing simple implemented. I would go for a more specialized
docking package like autodock, unless you want to build it in... It
wouldn't be that hard, and a lot faster to run probably...
> Thanks in advance,
> Paul Czodrowski
> Department of Molecular Pharmacology
> Biomedical Center
> Box G-B4, Brown University
> Providence, Rhode Island 02912 USA
> voice: +1 401 863 9841
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Dr. David van der Spoel, Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576, 75123 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://zorn.bmc.uu.se/~spoel
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