[gmx-users] Query: regarding how to include crystal water of pdb file as TIP4P water molecule

Mark Abraham mark.abraham at anu.edu.au
Sun Aug 1 10:46:03 CEST 2010

----- Original Message -----
From: bipin.singh at research.iiit.ac.in
Date: Sunday, August 1, 2010 17:15
Subject: [gmx-users] Query: regarding how to include crystal water of pdb file as TIP4P water molecule
To: gmx-users at gromacs.org

> Hi all,
> I am facing problem during the grompp step as in the topology file
> the crystal water and solvent water molecules added during solvation
> of the box are being treated as two different solvent in gromacs and
> showing error that the 
> Fatal error:
> number of coordinates in coordinate file (input.pdb, 32310)
>              does not match topology (input.top, 31578)

This was not the output of the grompp command below, because a filename is wrong. Please be sure you are matching the right files with  the right commands with the right output.


> I have followed following step:
> pdb2gmx -f input.pdb -water tip4p -o input_step1.pdb -p input.top
> editconf -bt dodecahedron -f input_step1.pdb -o input_step2.pdb -
> c -d 0.9
> genbox -cp input_step2.pdb -cs tip4p.gro -o input_b4em.pdb -p 
> input.top
> grompp -f em.mdp -c input_b4em.pdb -p input.top -o input_em.tpr
> I have checked all previous posts but none of them states this 
> problem explicitly
> and i also try all sort of possible ways to include it but i 
> did'nt got success.
> Please help me to resolve this problem.
> Regards
> Bipin
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