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

From: JiYuan Liu <>
Date: Fri, 30 Dec 2011 22:37:37 +0800

Hi Ben,

I have performed antechamber a second time with the "-nc -2" flag set,I
compared the two calib.xml,I found that the value of atmCharge=" " are
difference for every atom in my ligand,the other parts is as same as
before.This difference could cause to the ligand deforming in minimization?

Best Regards

于 2011年12月30日 22:12, Ben Roberts 写道:
> Hi JiYuan,
> On 30/12/2011, at 8:03 AM, JiYuan Liu wrote:
>> Thank you very much for these so detailed mailing list etiquette,I have
>> studied more about it.Please forgive me who is a beginner for maillist,I
>> will pay more attention in the next time.
> I understand. I was inexperienced in these matters once, too :-)
>> Do you think the wrong calib.xml is a crucial reason that related to the
>> ligand deforming in the minimization?
> I don't know without more information. Did you do what I suggested, i.e., run antechamber a second time with the "-nc" flag set, work up a new calib.xml, and compare it to your existing calib.xml? If so, what did you discover?
> Regards,
> 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 Fri Dec 30 2011 - 07:00:02 PST
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