Dear GROMACS list members,
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. I wanted to include PBC in my simulation, I want to know that does Gromacs by default use the option by minimum image convention or we have to edit pr.mdp & md.mdp by writing PBC=xyz ,How can I know that PBC is being included in my simulation? In spite of having dssp and running it I can not get the .xpm files. Instead while dssp is going on some kind of files namely ddEZ117f ddOWnvlx are being produced.How can I generate those xpm files? 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