[gmx-users] MD localized in the active site

[Erik Marklund]

Anna Marabotti skrev:
> Dear gmx-users,
> I'd like to perform a molecular dynamics simulation on a 
> protein-ligand complex, in such a way that only residues belonging 
> to the active site can move, whereas the rest of the protein is kept 
> fixed. I searched for some information about how to do it with 
> GROMACS, but I didn't find anything. 
> Could anybody give me some suggestions about this subject, please?
> Many thanks in advance and regards.
> Anna
> __________________________________________________________________
> Anna Marabotti, Ph.D.
> Laboratory of Bioinformatics and Computational Biology
> Institute of Food Science - CNR
> Via Roma, 64
> 83100 Avellino
> Phone: +39 0825 299651
> Fax: +39 0825 781585
> E-mail: amarabotti at isa.cnr.it <mailto:amarabotti at isa.cnr.it>
> Skype account: annam1972
> Web site: http://bioinformatica.isa.cnr.it/anna/anna.htm
>  
> "If you think you're too small to make a change, try sleeping with a 
> mosquito"
>  
Look for "freeze groups".

-- 
-----------------------------------------------
Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,    75124 Uppsala, Sweden
phone:    +46 18 471 4537        fax: +46 18 511 755
erikm at xray.bmc.uu.se    http://folding.bmc.uu.se/