[gmx-users] (no subject)

vincenzo venditti vincenzovenditti at hotmail.com
Wed Nov 24 17:50:20 CET 2004

If you ara running gromacs in windows, genbox command rename your topology 
as temp.top, so in the original topology no coordinates are found

>From: Xavier Periole <x.periole at chem.rug.nl>
>Reply-To: Discussion list for GROMACS users 
<gmx-users at gromacs.org>
>To: SLN Prasad Reddy <sreeyapu at rediffmail.com>,Discussion list for 
GROMACS users <gmx-users at gromacs.org>
>Subject: Re: [gmx-users] (no subject)
>Date: Wed, 24 Nov 2004 17:16:20 +0100
>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,
>>             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
>You have to include the solvent atoms in the topology.
>   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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