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

From: JiYuan Liu <>
Date: Sat, 31 Dec 2011 12:02:35 +0800

Hi Ben,

I think that I must redo all the procedure of MCPB with the "-nc -2"
flag set for the ligand,it would take me one or two weeks for the
gaussian calculation,as soon as I get the results I will tell you at once.

Happy New Year:-)

于 2011年12月30日 23:20, Ben Roberts 写道:
> On 30/12/2011, at 10:12 AM, JiYuan Liu wrote:
>> Hi Ben,
>> When I used the wrong calib.xml to perform the minimization,I have done
>> your suggestion,the step by step minimization is showed that the one of
>> the metal ion ZN2+ have a large force to attract the furanic ring oxygen
>> of the ligand,then the furanic ring was moved right and left until my
>> ligand was deformed in that position.
> And which components of the total potential energy are implicated here? The bonds? Angles? Torsions? Something else?
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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 Fri Dec 30 2011 - 20:30:03 PST
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