[gmx-users] Re: The WARNING

[Vitaly Chaban]

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...

Vitaly

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.
>>
>>
>> --