Re: [AMBER] Making a complex

From: Saaz Sakrikar <>
Date: Thu, 2 Aug 2012 16:30:49 +0530

The problem is I was told to dock the ligand with the macromolcule using
autodock and then save the best docked conformation and calculate the RESP
charge for the ligand *alone* using Gaussian. So then putting them back
together becomes a problem...I have since tried using a few different basis
sets for the RESP calculation and though the situation has improved its not
perfect yet.

I'm sorry for the absurdly late reply; actually I had created a new account
for the mailing list and forgotten the password!

Thanks again,

On Sat, Jun 23, 2012 at 7:07 PM, David A. Case <>wrote:

> On Sat, Jun 23, 2012, Saaz Sakrikar wrote:
> > I made the ligand prepin and frcmod files, and loaded the ligand and
> > receptor onto leap.
> >
> > Now I have been told to use "complex = combine {ligand receptor}".
> This is rarely a good strategy. I think what most people do is this:
> create
> a PDB file with both the ligand and the receptor in the proper positions.
> Put a TER card between the receptor and the ligand. Then use loadPdb to
> load the entire system into LEaP.
> ...dac
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Received on Thu Aug 02 2012 - 04:30:03 PDT
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