[gmx-users] grompp fatal error

Florian Haberl Florian.Haberl at chemie.uni-erlangen.de
Thu Nov 25 10:37:23 CET 2004


On Thursday 25 November 2004 10:06, SLN Prasad Reddy wrote:
> Dear Gromacs users,
> I installed gromacs 3.1 and working on a protein having 247 amino acids
> ,ATP and Mg++. I could generate waterbox by using genbox command. When i
> used "grompp" command to generate "xxx.tpr" to use with "genion" ,it is
> showing following error.
> Fatal error: number of coordinates in coordinate file (box.pdb, 24489)
> does not match topology (nbd.top, 0)

You should try this with your generated .gro file, and check if you are using 
the right files.

> I checked the number of coordinates in "box.pdb" and "nbd.top" and they are
> verymuch same.
> Kindly suggest me a solution. your suggestion will help me greatly.

Please be more specific with your error.

Have you "worked" like the flow chart said ?

> Many thanks in advance
> prasad.



 Florian Haberl                            Universitaet Erlangen/
 Computer-Chemie-Centrum    Nuernberg
                                                      Naegelsbachstr. 25
                                                      D-91052 Erlangen
  Mailto: florian.haberl AT chemie.uni-erlangen.de

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