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

From: JiYuan Liu <>
Date: Mon, 19 Mar 2012 20:51:51 +0800

Hi Ben,

Thank you for your reply.I tried more and more methods to check the
reasons for the distorsion of the ligand in the MD period before you
answered this question,finally I found that the lib.xml of the ligand
is a main element:

1. If I used gaussian to generate the RESP charge for the ligand,and via
antechamber to get the file named ligand.prein,then changed this file
into ligand-lib.xml by prep2xml.
2. If I used antechamber to generate ligand.prein directly by the charge
AM1-BCC,then changed this file into ligand-lib.xml also by prep2xml.

I found the difference from the two methods above,these methods involved
to the charge value with the metal ions and the ligand in the file named
*_chg2.prep,so they can effect the rationality of all MD process,the
second method in my opinion is very well, actually it could conserve the
X-ray structure.

Best Regards

> 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,
> Ben
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Jiyuan Liu
Key Laboratory of Plant Protection Resources and Pest Management,National Ministry of Education
Northwest A&F University
Yangling, Shaanxi
China 712100
Phone: 86-29-87092190
AMBER mailing list
Received on Mon Mar 19 2012 - 06:00:05 PDT
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