[gmx-users] Re: Connecting sidechains in gromacs file
zns at duke.edu
Fri Jul 15 20:34:02 CEST 2011
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?
> Zack Scholl
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