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

[David]

On Sun, 2004-09-19 at 16:12, 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)



check earlier messages from grompp. maybe the cpp can not be found.
(manual chapter 5)

> -----
> #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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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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