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

Shay Teaching shay.teaching at gmail.com
Sun Aug 1 10:15:23 CEST 2010

Dear Bipin,

Why not just erase the water molecules from the crystal?
You can do this before the pdb2gmx step and then, when you solvate the box
with genbox you'll have only one type of water both in the gro and topology
file. That's at least one way to deal with it.


On Sun, Aug 1, 2010 at 9:58 AM, <bipin.singh at research.iiit.ac.in> wrote:

> 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)
> 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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