Re: [AMBER] How to derive dihedral angle force constants by MCPB

From: Ben Roberts <>
Date: Thu, 23 Aug 2012 10:50:15 +1200

Hi JiYuan,

I encourage you to look at the original MCPB paper ( as well as a paper cited therein by Hoops et al. ( Basing their decision on the findings of Hoops et al., Peters et al. made the assumption (in MCPB) that torsional angles can be ignored. If this is not the case for your system, you will need to derive your own torsional parameters; MCPB can't help you with that step.

When you say "the water molecule…could not be stable…", what exactly do you mean? I find this sentence extremely vague. If you would like better help, please describe the instability. For example: "The hydrogen atoms of the water molecule collapse into the oxygen atom," or, "The water molecule adopts an almost linear geometry with an angle of 175°," or, "The water molecule moves away from the metal ion."

Finally, asking us to "please help me" is not encouraging. Again, please say what kind of help you would like. Do you have a specific question that needs answering? If so, please ask that specific question. Would you like instructions? We may be able to point you to an instruction manual or tutorial.


On 22/08/2012, at 8:20 PM, JiYuan Liu wrote:

> Hi,
> I have obtained bond and angle force constants by MCPB. My metal center
> included a small molecule and a water molecule. The water molecule that
> only have the bond and angle force constants could not be stable in MD
> simulation, so I need MCPB to derive the dihedral force constants.Please
> help me,thank you very much.
> Best Regards
> JiYuan
> --
> 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

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Received on Wed Aug 22 2012 - 16:00:03 PDT
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