[gmx-users] Re: The WARNING

Tsjerk Wassenaar tsjerkw at gmail.com
Thu Aug 21 10:26:40 CEST 2008


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.


On Thu, Aug 21, 2008 at 10:12 AM, Vitaly Chaban
<chaban at univer.kharkov.ua> wrote:
>> WARNING: masses will be determined based on residue and atom names,
>>         this can deviate from the real mass of the atom type
>> Is this warning serious?
>> Could any one tell me how to fix the warning?
>> I see nothing wrong with my .top and my .gro file.
> You should have right masses in your .top file - it's serious for
> adequate simulation.
> If you get this warning NOT WITH GROMPP but while constructing  a
> system it's not critical. Provide a valid .top file for the utility
> generating the warning.
> --
> Vitaly V. Chaban
> School of Chemistry
> National University of Kharkiv
> Svoboda sq., 4, Kharkiv 61077, Ukraine
> email: chaban at univer.kharkov.ua
> skype: vvchaban
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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

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