hi, On Friday 19 January 2007 15:25, sangeeta wrote: > Dear Sir, > > I have three questions, > > My protein has +2 charge, so I added two Cl atoms through the program > genion and subsequently edited the topol.top file, in spite of that while > running mdrun it gave an error that "FATAL error, CL atom type can not be > found",I can not understand the problem.
You have to add it to your .mdp file, too. > I wanted to include PBC in my simulation so in the pr.mdp file as well > in md.mdp file I wrote PBC=xyz , am I correct? How can I know that PBC is > being included in my simulation? Yes, take a look at mdout.mdp > In spite of having dssp and running it I can not get the .xpm files. > How can I generate those files? do_dssp -h (set proper path to dssp binary) > Waiting for your reply. > > > regards > SANGEETA > > -- > Open WebMail Project (http://openwebmail.org) > > _______________________________________________ > 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 Greetings, Florian -- ------------------------------------------------------------------------------- Florian Haberl Computer-Chemie-Centrum Universitaet Erlangen/ Nuernberg Naegelsbachstr 25 D-91052 Erlangen Telephone: +49(0) − 9131 − 85 26581 Mailto: florian.haberl AT chemie.uni-erlangen.de ------------------------------------------------------------------------------- _______________________________________________ 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