[gmx-users] Re: The WARNING

Vitaly Chaban chaban at univer.kharkov.ua
Thu Aug 21 10:38:46 CEST 2008

Tsjerk, probably you are right about grompp. I thought the user had
received this warning when preparing a system. Like genbox and so
on... So, I mean maybe he had not .tpr at that moment...


2008/8/21 Tsjerk Wassenaar <tsjerkw at gmail.com>:
> Vitaly,
> 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.
> Tsjerk
> 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.
>> --

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