Thanks Baofu. It seems that my topology file indeed is missing bonds for the sidechains! I am using a webtool so I am wondering whether the tool does not support these residues.
> are you sure that your topology file is correctly written? On 07/15/2011 11:34 AM, Zack Scholl wrote: > Hi all - > > I'm running a simulation that has an implicit solvent. I ran my > simulation and it seems that everything not connected to the backbone > has floated off into space. Is there a way to define connections so > that side chains stay connected? Has anyone had this problem before? > > Thanks, > > Sincerely, > Zack Scholl -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
