Hi Mark: Thank you for your interest. No, it does not work without the constraint. the dummy atom still collapsing with the ND atom. Also I try: [ constraint ] ; ai aj funct b0 ND CON 2 0.064381
But grompp give me the following error: Cleaning up constraints and constant bonded interactions with dummy particles ERROR: Cannot have constraint (86-87) with dummy atom (87) Fatal error: There were 1 dummy atoms involved in constraints Also I try to put all the [ dummies2 ] and [ constraints ] after the bonding information with the same result, the collapsing of the dummy atom. What could be the problem??? Anthony On Tuesday 06 February 2007 8:08 pm, Mark Abraham wrote: > Anthony Cruz wrote: > > Hi Users: > > > > > > In my topology before all the bonded information I add the following > > lines with the appropiate numbers: > > > > [ dummies2 ] > > ;Dummy from funct a > > CON ND OE 1 0.064381 > > > > [ constraint ] > > ; ai aj funct b0 > > ND OE 2 0.12032 > > > > The problem is that the dummy colapse with the ND atom during the EM. > > What could be the problem? I need to add the dummies2 section in my > > topology if it is present in the residue topology and it is present in my > > pdb??? > > Does it work without the constraint? > > Mark > _______________________________________________ > gmx-users mailing list [email protected] > 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 _______________________________________________ gmx-users mailing list [email protected] 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
