[gmx-users] Problem with X2top command

[David van der Spoel]

krithika krishnaswamy wrote:
> Hello,
> 
> I have a problem in the generation of the topology file of a ligand
> using x2top program..I am
> using the version 3.3.3 of Gromacs.
> 
> Here is the command that i used and the error am getting,
> 
> x2top -f chop.pdb -o dpppc.top
This program has limited use for small molecules but definitely not for 
a whole simulation system. Please look into other topology generating 
tools, e.g. pdb2gmx for proteins.

> 
> Can not find forcefield for atom OW-16850 with 2 bonds
> Can not find forcefield for atom OW-16853 with 2 bonds
> Can not find forcefield for atom OW-16856 with 2 bonds
> Can not find forcefield for atom HW1-16859 with 0 bonds
> Can not find forcefield for atom OW-16860 with 2 bonds
> Can not find forcefield for atom OW-16863 with 2 bonds
> Can not find forcefield for atom OW-16866 with 2 bonds
> Can not find forcefield for atom OW-16869 with 1 bonds
> Can not find forcefield for atom OW-16871 with 2 bonds
> Can not find forcefield for atom OW-16874 with 2 bonds
> 
> -------------------------------------------------------
> Program x2top, VERSION 3.3.3
> Source code file: ../../../../src/kernel/x2top.c, line: 206
> 
> Fatal error:
> Could only find a forcefield type for 8966 out of 16876 atoms
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-- 
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se