[gmx-users] Re: The WARNING

Tsjerk Wassenaar tsjerkw at gmail.com
Thu Aug 21 21:46:57 CEST 2008


A .gro file does not have information regarding masses. Therefore, any
operation involving masses (mass-weighted fitting) will not be
performed optimally.



On Thu, Aug 21, 2008 at 9:19 PM, Chih-Ying Lin <chihying2008 at gmail.com> wrote:
> Hi
> As you described.......
> This is not a grompp warning, but a warning from one of the analysis
> tools. grompp will never take masses 'out of the blue', but will
> always use the force field description (atom type definitions) or the
> mass specified in the .top/.itp file. It will bail out if no mass is
> properly defined for a specified atom. As David pointed out, these
> tools would benefit from reading in a .tpr (run input) file, not a
> .top file.
> 1. If I have the correct information in my .top file and .gro file,
> I could successfully run "GROMPP" command without the warning.
> And, I could ignore the warning from the analysis tools.
> right?
> 2. you described " these tools would benefit from reading in a .tpr
> (run input) file, not a .top file.......... "
> how about the .gro file? I see nothing wrong with my .gro file.
> Thank you
> Lin

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

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