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 23:12:08 +0800

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.

Best Regards

于 2011年12月30日 22:57, Ben Roberts 写道:
> 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.)?
> Cheers,
> Ben
> _______________________________________________
> AMBER mailing list

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 - 07:30:02 PST
Custom Search