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 09:57:36 -0500

Hi JiYuan,

On 30/12/2011, at 9:37 AM, JiYuan Liu wrote:

> 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?

Possibly. When you do a minimisation with energies reported every step (as I suggested in an earlier email), what do you see happening to the individual energy terms (BOND, ANGLE, etc.)?

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Received on Fri Dec 30 2011 - 07:00:03 PST
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