Subject: summary of "grid representation of protein potential"

From: Zhang HongYu <[email-masked]>
Date: Wed, 12 Jul 1995 09:34:31 +0900

Hi, 

Thanks to all the replies concerning my question of

"Grid representation of protein potential".

>Is there any code available which represents the force field
>(such as ECEPP,CHARMm) or molecular volume of a protein by a grid?

Here is a summary and welcome more infomation if any.

----------------------------------------------------------------------------------

From: Nathaniel (noj) Malcolm <[email-masked]>

 I reccomend that you have a look at the work of A. Warshel,
he has been using Langevin Dipoles on a grid to 
represent proteins and solvents for some time.
	Noj
	[email-masked]

From: Mr Andrew D Allen <[email-masked]>

Dear Henry Hongyu Zhang,

	Try contacting :-

		[email-masked],
		[email-masked] (Nick Hodge),
		[email-masked] (Tom Thacher)

	They are working on BForce, which should go into the Biosym
software suite, (hopefully for the next release). The preliminary
information seems to fit what you are looking for.

Andy

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From: [email-masked] (Pieter Stouten)

Dear HongYu,

At 11:21 95/07/02, you wrote:

>Is there any code available which represents the force field
>(such as ECEPP,CHARMm) or molecular volume of a protein by a grid?
>
I am not sure exactly what you are looking for. I assume you want to do EM
or MD with a grid representation of (the bulk of) a protein. We have
developed a method that is currently implemented in Amber and Biosym's
Discover. Relevant papers are:

* P.F.W. Stouten, C. Frvmmel, H. Nakamura & C. Sander, "An Effective
  Solvation Term Based on Atomic Occupancies for Use in Protein
  Simulations," Mol. Simulation 10 (1993) 97-120.
* B.A. Luty, Z.R. Wasserman, P.F.W. Stouten, C.N. Hodge, M. Zacharias &
  J.A. McCammon, "A Molecular Mechanics/Grid Method for Evaluation of
  Ligand-Receptor Interactions," J. Comp. Chem. 16 (1995) 454-464.

Please let me know if you would like to receive reprints.

Cheers, Pieter.

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From: wujih <[email-masked]>

Hello, Mr. zhang, it is nice to see the email from china. 
As for your question, what do you actually means when you say 'to 
represent the force field or molecular volume of a protein? is it to 
map them on a grid?  Do you got UHBD4.01 or Python program? Have a try. 

Cheers, 

Wu J H     PhD in computer modelling

Chem. Department
Univ. of Essex
Colchester  CO4 3SQ 
U.K.

email   [email-masked]