[gmx-users] Question about fatal error of .gro and .top files

Tomohiro Hayashi hayashi at echem.titech.ac.jp
Sun Sep 19 16:12:26 CEST 2004

Hi Gromacs Users,

I've just started using Gromacs ver. 3.2.1 on Mac OS X Panther 
(10.3.5). The installation was successful. But now I'm facing one 
problem in testing tutorial examples.

I always get same problem in following examples (water and speptide) 
just as written in the getting started manual:

in the case of water
Fatal error: number of coordinates in coordinate file (conf.gro, 648)
              does not match topology (topol.top, 0)
and in the case of speptide
Fatal error: number of coordinates in coordinate file (b4em.gro, 2741)
              does not match topology (speptide.top, 0)
The program always says the number of atoms equal to 0 from .top files, 
although the number of atoms is indicated in the .top file, as shown 
below (topol.top in the case of water)
#include "ffgmx.itp"
#include "spc.itp"

[ system ]
Pure Water

[ molecules ]
SOL 216
Did anyone have the same problem?? I think this is not a difficult 

Thanks in advance,
Tomohiro Hayashi
Postdoctoral Fellow
Hara Lab
Department of Electronic Chemistry,
Interdisciplinary Graduate School of Science and Engineering, Tokyo 
Institute of Technology
snail mail: G1-1008 4259 Nagatsuta-cho Midoriku Yokohama-shi, 226-8502, 
tel&fax: +81-45-924-5439
e-mail: hayashi at echem.titech.ac.jp

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