Re: [AMBER] Constant pH with ligand

From: FyD <>
Date: Wed, 16 Oct 2013 07:25:53 +0200

Dear Nicole,

if you need to generate a new FF library for your molecule you might
be interested in using the R.E.D. tools and/or R.E.D. Server.
Tutorials are also available at

regards, Francois

> 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?

AMBER mailing list
Received on Tue Oct 15 2013 - 22:30:03 PDT
Custom Search