----- Original Message ----- From: [email protected] 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: [email protected]
> 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. Mark > > 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
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