[gmx-users] crystal water

Maik Goette mgoette at mpi-bpc.mpg.de
Thu Sep 8 11:51:12 CEST 2005


If its a crystal water from the x-ray structure, it will be included 
automatically by pdb2gmx. If you want to place a new hydrogen, it may be 
a bit more difficult because of the missing coordinates. Perhaps you 
should try to fill the box with water and hope, that one water sits in 
the place, you want it to.
Hmm...I would suggest to make a short mdrun and have a look, if your 
water moves away from the location, and if another takes its place.
If it moves away and no other water will take its position, it may be 
useful to restrain it.


Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
37077 Goettingen
Tel.  : ++49 551 201 2310
Fax   : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
WWW   : http://www.mpibpc.gwdg.de/groups/grubmueller/

Joanne Hanna wrote:
> Hi 
> If i am wanting to include a single water molecule, thought to make a hydrogen bond between my enzyme and the substrate, into my simulation, before i solvate the system, how do i do this? also is it advisable to keep this water molecule fixed throughout the simulation?
> Many thanks for any advice.
> Jo
> Joanne Hanna
> Department of Chemistry
> University of Warwick
> Coventry
> CV4 7AL
> J.F.Hanna at warwick.ac.uk
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