[gmx-users] adding ions in Gromacs 4.6.5

[soumadwip ghosh]

Justin,
           I have used the paramchem software as suggested by you. I
submitted my pdb file and CGENFF gave a .str file as output. Now could you
please tell me how to proceed to obtain the .itp file? Also is it sensible
to use SWISSPARAM since it gives .itp from .mol2 directly? Once I have the
.itp file, I should include it to the .top file before adding the species
via -ci and -nmol of genbox right?
My questions might sound very basic and lame but I am not a professional in
GROMACS. Please help.

Thanks and regards,
Soumadwip