[gmx-users] Fatal error: Could only find a forcefield type for 106 out of 270 atoms

[David van der Spoel]

darrellk at ece.ubc.ca wrote:
> Could you please let me know why GROMACS is able to find forcefields for
> only 106 of the 270 atoms. My .gro file is a model of a graphene
> structure with 211 equally spaced carbon atoms with the remaining
> hydrogen atoms also equally spaced from the carbon atoms to which they
> are bonded. Here is a sample output:
> 
> ********************************************************************
> Can not find forcefield for atom C-208 with 3 bonds
> Can not find forcefield for atom C-209 with 3 bonds
> Can not find forcefield for atom C-210 with 3 bonds
> Can not find forcefield for atom C-211 with 3 bonds
> 
> -------------------------------------------------------

you probably want to play with the ffoplsaa.n2t file a bit to make this 
work, but it should be possible.


> Program x2top, VERSION 3.3.3
> Source code file: x2top.c, line: 206
> 
> Fatal error:
> Could only find a forcefield type for 106 out of 270 atoms
> -------------------------------------------------------
> ********************************************************************
> 
> Thank you in advance for your assistance.
> 
> Darrell Koskinen
> MASc Candidate
> University of British Columbia
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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