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
--
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
