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

From: Ben Roberts <>
Date: Fri, 30 Dec 2011 09:12:34 -0500

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?


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Received on Fri Dec 30 2011 - 06:30:02 PST
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