[gmx-users] Re: Connecting sidechains in gromacs file

Zack Scholl 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?
> Thanks,
> Sincerely,
> Zack Scholl

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