한상화 wrote: > Dear Gromacs users, > > > > I have gone through all the way to the final product MD, where I > received the following error message for grompp. > > The same topology file pn.top did not give me any problem in the > previous steps including grompp with pr.mdp or grompp with em.mdp.
The problem doesn't look like it's actually the topology... that was just the last thing that grompp looked at. > I included solvent and ions in the md.mdp file for temperature control. > > Any comments would be greatly appreciated. > [EMAIL PROTECTED] papain]# grompp -f md.mdp -c pn_md.pdb -r pn_md.pdb -p > pn.top > -o pn_md.tpr* This isn't your problem, but it is a *really bad idea* to do daily work as root. See here for info and discussion why... http://en.wikipedia.org/wiki/Superuser > > ' for variable integrator, using 'md' > > Next time use one of: 'md' 'steep' 'cg' 'bd' 'sd' 'nm' 'l-bfgs' 'tpi' > > ' for variable ns-type, using 'Grid' > > Next time use one of: 'Grid' 'Simple' > > ' for variable coulombtype, using 'Cut-off' > > Next time use one of: 'Cut-off' 'Reaction-Field' > 'Generalized-Reaction-Field' 'PME' 'Ewald' 'PPPM' 'Poisson' 'Switch' > 'Shift' 'User' 'Generalized-Born' 'Reaction-Field-nec' 'Encad-shift' > 'PME-User' > > ' for variable optimize_fft, using 'no' > > Next time use one of: 'no' 'yes' > > ' for variable tcoupl, using 'No' > > Next time use one of: 'No' 'Berendsen' 'Nose-Hoover' 'yes' 'Andersen' > 'Andersen-interval' > > ' for variable Pcoupl, using 'No' > > Next time use one of: 'No' 'Berendsen' 'Parrinello-Rahman' 'Isotropic' > > ' for variable gen-vel, using 'no' > > Next time use one of: 'no' 'yes' > > ' for variable constraints, using 'none' > > Next time use one of: 'none' 'h-bonds' 'all-bonds' 'h-angles' 'all-angles' > > > > Back Off! I just backed up mdout.mdp to ./#mdout.mdp.2# > > WARNING 1 [file pn_md.mdp, line unknown]: > > Unknown left-hand 'warnings' in parameter file > This is being caused by gibberish in your .mdp file. Fix that first. Mark _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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
