[gmx-users] grompp error

Erik Lindahl lindahl at sbc.su.se
Fri Oct 14 22:09:38 CEST 2005

Hi Ken,

Please try it with the released 3.3 version - we've ironed out quite  
a few bugs since the beta you're using.

Also, any bugs reported against 3.3 the next week or so will be fixed  
almost instantly so we can release a more stable 3.3.1.



On Oct 14, 2005, at 9:19 PM, Ken Rotondi wrote:

> Hello All,
> Okay, I'm going to scream. I've made up a .gro and .top file for a  
> system I'm working on. I e-minimized and equilibrated the system  
> successfully. I'm trying to start the run (using the same .top file  
> I used in the set-up) and I receive a grompp error:
> _______________________________________________
> Program grompp, VERSION 3.3_beta_20050202
> Source code file:  grompp.c, line: 427
> Fatal error:
> number of coordinates in coordinate file (x.gro, 172177)
>         does not match topology (x.top, 0)
> _______________________________________________
> Also lots of strange chatter in the output, such as:
> ' for variable ns-type, using 'Grid'
> Next time use one of: 'Grid' 'Simple'
> There are 10 of these 'warnings' and in each case the variable used  
> is one of the available variables.
> The big problem is that the end of the .top file, quite clearly the  
> [molecules] section shows 1 protein and 56926 SOL
> I've checked all the input files in vi, they're all clean text

Ah, that explains it. Gromacs is only compatible with emacs ;-)



Erik Lindahl  <lindahl at sbc.su.se>
Assistant Professor, Stockholm Bioinformatics Center
Stockholm University, SE 106 91 Stockholm
Phone: +46 8 5537 8564     Fax: +46 8 5537 8214

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