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

[Justin A. Lemkul]

Yi Gao wrote:
> 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!
> 

There is no need to do any of this.  Just #include "spc.itp" in your topology. 
See the manual for details, as well as:

http://www.gromacs.org/Documentation/Include_File_Mechanism

-Justin

> Best,
> Yi
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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