Re: AMBER: target MD simulation

From: David A. Case <>
Date: Wed, 27 Aug 2003 13:39:31 -0700

On Wed, Aug 27, 2003, Lishan Yao wrote:

> I tried target MD once. I use GBSA model. Seems to me, the simulation
> is quite slow. My system is a protein ligand complex about 1000 a.a.. I
> pulled the ligand out. I talked with one of my friend. He thinks that
> each time when amber superimposes the current structure with target
> structure, it is quite expensive.

Is this not something you can easily find out for yourself? Run a short
simulation with and without targetted restraints, and see what the time
differences are.

[No GB simulation of a protein of 1000 residues is going to be very fast...]


David A. Case                     |  e-mail:
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
10550 N. Torrey Pines Rd.         |  home page:                   
La Jolla CA 92037  USA            |
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Received on Wed Aug 27 2003 - 21:53:01 PDT
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