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 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 > <[EMAIL PROTECTED]> 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. >> >> >> -- _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
