[gmx-users] Re: x2top problem of dealing with spc216 water

[Vitaly Chaban]

> Hi, I used x2top to generate spc216.top. The spc216.gro file comes from
> Gromacs tutor directory. I use Gromacs 4.0.5 version. The command line is
> x2top -f scp216.gro -o scp216.top. The error message is
>
> Can not find forcefield for atom OW-1 with 2 bonds
> Can not find forcefield for atom OW-4 with 2 bonds
> Can not find forcefield for atom OW-7 with 2 bonds
> Can not find forcefield for atom OW-10 with 2 bonds
> Can not find forcefield for atom OW-13 with 2 bonds
> Can not find forcefield for atom OW-16 with 2 bonds
> Can not find forcefield for atom OW-19 with 2 bonds
> Can not find forcefield for atom OW-22 with 2 bonds
> Can not find forcefield for atom OW-25 with 2 bonds
> Can not find forcefield for atom OW-28 with 2 bonds
> Can not find forcefield for atom OW-31 with 2 bonds
> Can not find forcefield for atom OW-34 with 2 bonds
> Can not find forcefield for atom OW-37 with 2 bonds
> ...
> -------------------------------------------------------
> Program x2top, VERSION 4.0.5
> Source code file: x2top.c, line: 207
>
> Fatal error:
> Could only find a forcefield type for 432 out of 648 atoms
> -------------------------------------------------------
> I don't want to use pdb2gmx to generate *.top file, because spc216 water is
> just a part of my system. Could anyone help me to resolve this problem?
> Thanks a lot!

Do not try to use x2top for small molecules. Even if you succeed,
you'll spend much time to edit this TOP file. It is definitely easier
to write it by hand at once. IMHO.

BTW, for SPC water, TOP file already exists in the topology folder.

--
Dr. Vitaly V. Chaban
Department of Chemistry
University of Rochester,
Rochester, NY, U.S.A.