[gmx-users] grompp fatal error

[Anton Feenstra]

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)

Possibly the pre-processor grompp uses to read in the .top file (and related
forcefiedl stuff) failed. Look for messages relating to 'cpp'. These are often
very cryptic, so if you cannot make it out, put them all in a mail to the list
(or, simply paste in all of grompp's output).


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra at few.vu.nl - www.few.vu.nl/~feenstra/         |
|             | "If You See Me Getting High, Knock Me Down" (RHCP)    |
|_____________|_______________________________________________________|