AMBER Archive (2009)

Subject: [AMBER] Any tutorial on the proper way to merge a ligand and protein?

From: Dean Cuebas (deancuebas_at_missouristate.edu)
Date: Wed Sep 09 2009 - 13:26:02 CDT

Dear all,

I see several posts whose general issue involves preparing a system with a
ligand and a protein.

Is there a tutorial that describes the steps needed to use leap to prepare
such a system?

One of the tutorials at the ambermd site shows the preparation of a ligand
and it's solvation, but does not show how to properly setup a system when
the coordinates of the ligand and protein are known.

This is exactly what I wish to do myself, and it is not obvious to me at all
how to accomplish this. I have a protein, and I can generate the files for
my ligand, but what next?

Thanks in advance for any suggestions, especially since I think that a large
fraction of amber users are interested in molecule to molecule interactions
in MD. I guess the bottom line is how does one setup a system with more than
one interacting molecule.

Regards,

Dean Cuebas

Dr. Dean Cuebas, Associate Professor of Chemistry
deancuebas_at_missouristate.edu, Ph 417-836-8567 FAX 417-836-5507
Dept. of Chemistry, Missouri State University
Springfield, Missouri 65897

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