On Tue, Oct 15, 2013 at 5:55 PM, Nicole Ippolito <
ippolito.nicole89.gmail.com> wrote:
> Hello,
>
> I am running constant pH on a system have substrates in the active site.
> Running the Apo structure was very straight forward but when running tleap
> with the substrates and the enzyme it does not recognize the atom type of
> the substrates. I think I need to go about setting up a topology file for
> the substrates, but I am not sure how I should do this. Is it done in a
> similar fashion as a regular MD run or is it a keyword in the tleap.infile?
>
I think what you're looking for is how to parametrize a new residue. There
is a tutorial for using antechamber to help with this process:
http://ambermd.org/tutorials/basic/tutorial4b/
In the future, it helps to know exactly what you tried and the exact error
messages you got if you want more specific help.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Tue Oct 15 2013 - 18:00:02 PDT
