[gmx-users] need help

Pradip Kumar Biswas p.biswas at csuohio.edu
Wed May 25 15:22:08 CEST 2005

Please check whether your "cpp" flag definition
in your executable "demo" script is:

cpp                 =  /lib/cpp

if so, change it
to:        cpp                 =  /usr/bin/cpp

Grompp preprocessor setup is not being able to
access the topology file created during pdb2gmx.

On May 25, 2005, at 3:18 AM, protim chakraborti wrote:

> Hello users
> I am stuck with problem running Gromacs. I am running this package in 
> Mac OS X.
> In the editconf option  I am centering my molecule with the following 
> options,
> editconf -box o -d 1.5 -f <input gro file name> -o <output file name>.
> Thereby the new dimensions are being printed on screen like new
> center, new box vectors etc. Later during grompp when I am giving the
> following command
> grompp -f -po -c <genbox ouput .gro file> -p <pdb2gmx output .top
> file>, it is giving me the following message :
> Fatal error: number of coordinates in coordinate file 
> (1AG9_genout.gro, 41)
>             does not match topology (1AG9.top, 0),
> Am i doing any mistake? If yes where, I am pondering for that myself.
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Pradip K. Biswas, PhD.
Research Associate, Department of Chemistry;
Cleveland State University, Ohio-44115
Phone: 1-216-875-9723
"Big thing in a Simpler way!!"
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