Subject: Summary: Monte Carlo

From: [email-masked] (Xiaoou Xiang)
Date: Thu, 9 Jun 94 21:51:01 -0400

Dear Netters:

I received many responses to my posting:

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>I posted this question earlier:

>>Could any of you tell me where to obtain Monte Carlo simulation programs for 
>>molecular mechanics calculations?

>Let me be more specific. I want to use Monte Carlo method to sample the 
>conformational space of a small drug molecule to find the global and local
>minima. The molecular mechanics programs I have are AMBER and CHARMM, none of
>which came with Monte Carlo utility.
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Here is a brief summary:

1. Most people recommended MacroModel for Monte Carlo search.

2. However, Mark Zottola, while commending MacroModel, finds the "polling" 
method of BioCAD/Catalyst (from MSI?) a more efficient search strategy.

3. "Monte Carlo Simulation for Liquids" by M. P. Allen and D. J. Tildesley, 
Oxford(1987) is the recommended book.

4. Contradicting info is passed to me about the availability of MC that go 
with CHARMM or AMBER. I'll let people in the know to clarify it.

5. Yvonne Martin recommends DGEOM from QCPE for conformational search.

6. Sybyl (Tripos) also does MC.

Many thanks to all who replied.

Phil Xiang
Biophysics program
Brandeis University