[gmx-users] solvent molecules between protein-peptide complex

Marc F. Lensink lensink at scmbb.ulb.ac.be
Mon Apr 18 13:09:42 CEST 2005

On Mon, Apr 18, 2005 at 03:54:45PM +0530, Alok wrote:
> hello gromax users,
>                               I have simulated a protein-peptide 
> complex solvated in water.
> Now i want to specifically analyse the number of solvent molecules 
> between the protein-peptide complex as a function of time.
> Is there any direct or indirect tool available in GROMACS to help me 
> carry out this analysis.
> Please suggest some solution.
> Thanking you all in advance.

i have a tool that may do what you want.  i've used it for
peptide/lipid interaction, to define the lipids that are under the
peptide.  as in a membrane simulation the normal to the bilayer is
typically the z-axis, you'll have to rotate your system to conform to
this convention.  i think you can do that by using editconf to
generate one such structure, and then with trjconv you fit all frames
to that reference structure.  contact me off-list if you want to get
the source of the program.

Marc F. Lensink           http://www.biochem.oulu.fi/~lensink/
SCMBB, Université Libre de Bruxelles   lensink at scmbb.ulb.ac.be
Boulevard du Triomphe - CP 263, B-1050 Brussels, Belgium
tel: +32 2 650 5411  secr: +32 2 650 2013  fax: +32 2 650 5425

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