AMBER Archive (2008)

Subject: Re: AMBER: about glycam06

From: WANG,YING (wangying_at_ufl.edu)
Date: Sat May 03 2008 - 18:55:11 CDT

Thanks a lot!!
I have one more question. The parameter of the lj potential of
glycam06 are the A, B parameters of the 12-6 equation: like
(A/rij^12)-(B/rij^6)
Or the epsilon and sigma in this form:
4*epsilon[(sigma/rij)^12-(sigma/rij)^6]?

Thanks!

Best,

Ying

On Sat May 03 19:49:27 EDT 2008, "David A. Case"
<case_at_scripps.edu> wrote:

> On Sat, May 03, 2008, WANG,YING wrote:
>
>> Some of the specific dihedral interactions have various values,
>> like
>> CK-CG-CG-N
>> , there are three values. Could anybody tell me the difference
>> between them? Which one I should use?
>
> You (or rather programs) use all three: this single torsion has
> three
> components (of different periodicities) -- the actual potential
> is the sum
> of all three terms.
>
> ...dac
>
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--
WANG,YING
Mechanical and Aerospace Engineering
University of Florida
Office: NEB 139
TEL: 001-352-846-3030

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