[gmx-users] grompp error

supti mukherjee suptimukherjee at gmail.com
Wed Nov 5 08:51:27 CET 2008

Dear all
I am facing a problem in gromacs-4.0 during grompp.

1. After Genbox command , when I am giving Grompp command,the coordinates of
top file and gro file are not matching.

2. I have tried following the same protocol in gromacs-3.3.3D. It went on
fine without any error.

3. Both the top files (across different versions of gromacs) however have
got the same content.The water box is being included in the top file as well
after genbox.

The error messege is like this.

Program grompp_d, VERSION 4.0
Source code file: grompp.c, line: 352

Fatal error:
number of coordinates in coordinate file (file_b4em.gro, 46634)
             does not match topology (file.top, 9977)
Does anybody throw some lights on it?

Supti Mukhopadhyay
PhD student
NIMHANS, Bangalore
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