Re: [AMBER] Which method is the best way to solve metalloprotein?MCPB or Only consider Electrostatic and VDW

From: Ben Roberts <>
Date: Mon, 19 Mar 2012 21:30:42 +1300

Hi JiYuan,

Again, I apologise for the delay. However on a question such as this, you would be better to address it to the list at large. There are other readers who are well qualified to answer questions about force fields, and you would get a quicker answer that way.

On 28/02/2012, at 10:16 PM, JiYuan Liu wrote:

> This distorsion like a cycle around equil and production period,some frames is well and some is distorted.I also sent one of the pdb of conformations with the small molecule(prod1-ca1.pdb) that be distorted and a initial small molecule pdb(ca.pdb) to you.Could the random distorsion for the small molecule conformation in all of the MD period belong to a normal situation?Please give some advises.

I'm not sure how you got your parameters, so I can't advise you fully. Did you use the GAFF force field, though, or one prepared using MCPB? It's possible that your angle force constants aren't strong enough. However, as I said in my earlier email, we aren't really in a position to validate your parameters for you. The matter's really in your hands. You have three options: Re-check your methods and make sure your choices were correct; use a different force field; or manually adjust the parameters and hope the revised parameters give physically sensible behaviour.

Good luck,

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Received on Mon Mar 19 2012 - 02:00:03 PDT
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