>
> 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?
>
If you have got .tpr submit it to the analysis tools.
--
Vitaly V. Chaban
School of Ch
Lin,
A .gro file does not have information regarding masses. Therefore, any
operation involving masses (mass-weighted fitting) will not be
performed optimally.
Cheers,
Tsjerk
On Thu, Aug 21, 2008 at 9:19 PM, Chih-Ying Lin <[EMAIL PROTECTED]> wrote:
> Hi
> As you described...
> This is not a
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 <[EMAIL PROTECTED]>:
> Vitaly,
>
> This is not a grompp warning, but a w
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
> 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 y
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