Re: [AMBER] Making a complex

From: David A Case <>
Date: Thu, 2 Aug 2012 08:00:52 -0400

On Thu, Aug 02, 2012, Saaz Sakrikar wrote:

> 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 don't understand why you have a problem. Presumably you have a pdb-format
file from Autodock that has the conformation you want. Just use that. The
fact that you also did some Gaussian calculations seems rather beside the
point. Or, maybe you can explain more clearly why the strategy outlined below
does not meet your needs.


> > 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.
> >

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Received on Thu Aug 02 2012 - 05:30:03 PDT
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