AMBER Archive (2003)

Subject: Re: ANAL in AMBER

From: David A. Case (case_at_scripps.edu)
Date: Fri May 09 2003 - 11:11:33 CDT

On Tue, May 06, 2003, A.Madhumalar wrote:

> I am trying to calculate energy of a nucleotide using ANAL module of
> amber, for that i have defined three groups phospate group alone, other
> sugar backbone atoms and base atoms.In the anal output, for phosphate
> group,the matrix looks as
>
> ENERGY CONTRIBUTION BY GROUPS
>
> GROUP BOND ANGLE DIHEDRAL VDW14 EEL14 VDWNB
> EELNB HBOND CONSTRAINT TOTAL
>
> 1 2.71 0.83 1.28 0.46 20.83 -1.76
> 15.57 0.00 0.00 39.922
>
>
> but in the other matrices
>
> VDW (N-B + 1-4) INTERACTION ENERGY MATRIX
> it is 0.00
>
> 1 2 3
>
> 1 0.000 -0.355 -0.575
>
> ELECTROSTATIC (N-B + 1-4) INTERACTION ENERGY MATRIX
>
> 1 2 3
>
> 1 0.000 -13.975 2.652
>
> 1 group defined is phosphate group, its VDW & EEL energy value is 0.00 in
> the component matrices, but it is nonzero in energy contribution by
> groups. can anyone tell me where i am wrong? How it is calculated? Thanks
> for any suggestion.
>

You can check the following, from the mail archive:

    http://structbio.vanderbilt.edu/archives/amber-archive/2002/0745.phtml

The easiest way to find things like this is a Google search:

    anal group site:structbio.vanderbilt.edu

The "site" is where the Amber mail archives are stored; the keywords can
be anything that seems relevant. This gives a nice set of hits.

..good luck..dac 

-- 

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David A. Case                     |  e-mail:      case_at_scripps.edu
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