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. > > > -- > Vitaly V. Chaban > School of Chemistry > National University of Kharkiv > Svoboda sq., 4, Kharkiv 61077, Ukraine > email: [EMAIL PROTECTED] > skype: vvchaban > _______________________________________________ > 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 > -- 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 _______________________________________________ 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
