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

From: FyD <>
Date: Tue, 20 Mar 2012 17:26:58 +0100

Dear JiYuan,

Considering the number of bugs/inaccuracies... available in
Antechamber, you might consider giving a try to R.E.D. Server or the
R.E.D. tools .

regards, Francois

> 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
> JiYuan
>> 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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Received on Tue Mar 20 2012 - 10:00:03 PDT
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