[gmx-users] how can i know the center of the cleft of protein?

[David van der Spoel]

Chih-Ying Lin wrote:
> Hi
> how can i know the center of the cleft of protein?
> I mean how to calculate or use Gromacs to know the center (x,y,z) of
> the cleft of protein?
This is an ill-defined problem. You could try g_traj with a suitable 
index file with the surrounding residues.
> 
> 
> Thank you
> Lin
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php


-- 
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se