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

[Zack Scholl]

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