[gmx-users] solvation of protein

[Srivastava, Dhiraj (UMC-Student)]

I am using the following commandfor solvating my protein but i am stiil getting my protein at one face of box.

editconf -bt octahedron -f trp2.pdb -o trp2.pdb -c -d 0.6


________________________________

From: gmx-users-bounces at gromacs.org on behalf of Haberl Florian
Sent: Sun 7/16/2006 6:55 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] solvation of protein



Hi,

> Hi
> when i am trying to solvate my protein in water box, i am not getting my
> protein in the center of but at one face of water box with some atoms
> outside waterbox. what should i do for this problem? should i move center
> of my protein to the center of water box using some tcl script in vmd?
> how can i include the crystallographic water in the *.gro file for
> simulation?

Use option -c for center in editconf it is also useful to add here
distance to box end

editconf -c -d 0.8

or something like this.

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greetings,

Florian

------------------------------------------------------------------------
 Florian Haberl              Universitaet Erlangen/Nuernberg
 Computer-Chemie-Centrum     Naegelsbachstr. 25, D-91052 Erlangen

 Mailto: florian.haberl AT chemie.uni-erlangen.de

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