[gmx-users] (no subject)

[Xavier Periole]

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 tried "grompp" command to get "xxx.tpr" to use with 
> "genion" command,it is showing following error.
>
>
> calling /lib/cpp...
> sh: /lib/cpp: No such file or directory
> cpp exit code: 32512
> Tried to execute: '/lib/cpp  -I/usr/local/share/gromacs/top -DFLEX_SPC 
> nbd.top > gromppAXEl1v'
> The '/lib/cpp' command is defined in the .mdp file
> processing topology...
> processing coordinates...
> Fatal error: number of coordinates in coordinate file (box.pdb, 24489)
>             does not match topology (nbd.top, 0)
>
> I checked the number of coordinates in "box.pdb" and "nbd.top" and 
> they are verymuch same.
>
> "grompp" seems to be not processing nbd.top.
>
> Kindly suggest me a solution. your suggestion will help me greatly.
>
> Many thanks in advance
>
> prasad.
>
You have to include the solvent atoms in the topology.

-- 
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   Xavier Periole - Ph.D.

   Dept. of Biophysical Chemistry / MD Group 
   Univ. of Groningen
   Nijenborgh 4
   9747 AG Groningen
   The Netherlands

   Tel: +31-503634329
   Fax: +31-503634800
   email: x.periole at chem.rug.nl
   web-page: http://md.chem.rug.nl/~periole
   
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