[gmx-users] grompp error

[Tsjerk Wassenaar]

hmm, okay, forget whatever you think I replied :)

On 11/5/08, Berk Hess <gmx3 at hotmail.com> wrote:
>
>  Hi,
>
>  There is a bug in the 4.0 grompp which causes problems when you have two
>  consecutive "blocks" with the same molecule type.
>  You will have to merge them into one block.
>
>  I have fixed this bug for the 4.0.1 release.
>
>  Berk
>
>  ________________________________
>  > Date: Wed, 5 Nov 2008 13:21:27 +0530
>  > From: suptimukherjee at gmail.com
>  > To: gmx-users at gromacs.org
>  > Subject: [gmx-users] grompp error
>
> >
>  >
>  > 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?
>  >
>  > Regards
>  > Supti Mukhopadhyay
>  > PhD student
>  > NIMHANS, Bangalore
>  > India.
>
>
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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623