Re: [AMBER] Constant pH with ligand

From: Jason Swails <>
Date: Tue, 15 Oct 2013 20:33:04 -0400

On Tue, Oct 15, 2013 at 5:55 PM, Nicole Ippolito <> 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:

In the future, it helps to know exactly what you tried and the exact error
messages you got if you want more specific help.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Tue Oct 15 2013 - 18:00:02 PDT
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