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

[bipin.singh at research.iiit.ac.in]

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