AMBER Archive (2006)

Subject: AMBER: from ADP-small protein complex to GTP-protein complex

From: Fenghui Fan (fenghui_fan_at_yahoo.com)
Date: Mon Sep 25 2006 - 23:00:53 CDT

Dear all,

There is a 3-D coordinates of a protein-ADP complex,
and I want to run the MD of the protein-ATP complex.
What I should mention is that the protein in the two
complexes are same, but we do not have the protein-ATP
coordinates. If we replace the ATP with ADP in the
protein-ADP complex coordinates, there will be aome
kind of protein ligand distance violation.

Can we still use the replaced protein-ATP 3-D
coordinates for MD in order to get the ATP-protein
structure?

I am looking forward to getting your reply.

Best regards.

Fenghui Fan

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