[gmx-users] need help

David van der Spoel spoel at xray.bmc.uu.se
Wed May 25 09:27:19 CEST 2005

On Wed, 2005-05-25 at 12:48 +0530, 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)
topology error. do you have a protein of 41 atoms? pdb2gmx can only do
> Am i doing any mistake? If yes where, I am pondering for that myself.
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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