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

[Kay Gottschalk]

change the mdp file from 'cpp                 =  /lib/cpp' to 'cpp      
            =  cpp'.
K.

On Sep 19, 2004, at 5:12 PM, Tomohiro Hayashi wrote:

> 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 
> problem.
>
> Thanks in advance,
> Tomo
> -----
> 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, Japan
> tel&fax: +81-45-924-5439
> e-mail: hayashi at echem.titech.ac.jp
>
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>
Dr. Kay-E. Gottschalk
Department of Biological Chemistry
Weizmann Institute of Science
Rehovot
Israel