Re: AMBER: question about periodicity of torsion parameter

From: Carlos Simmerling <>
Date: Fri, 18 Mar 2005 17:51:40 -0500

what it means is that the absolute value of pn is used for the
energy evaluation, the negative sign means that there are more

Carlos L. Simmerling, Ph.D.
Associate Professor Phone: (631) 632-1336
Center for Structural Biology Fax: (631) 632-1555
Stony Brook University Web:
Stony Brook, NY 11794-5115 E-mail:
=================================================================== wrote:

>Dear all,
>According to the Amber manual and the paper, when PN (periodicity) for
>torsion is negative, "it is not used in the calculation but signifies more
>than one component around a given bond". So negative PN is just an
>indicator. But in the energy calculation, we need PN to calculate trosion
>potential for each term (V1, V2, V3...). So my question is isn't there
>missing PN (because negative PN is only indicator)? And how should I
>choose the order to list those V1, V2, V3 terms?
>For example, I have a torsion potential which can be deconvoluted into 3
>terms (V1, V2, V3). So I have to assign the first 2 PN values to negative
>and the last one is positive. But how should I choose the order? If I
>choose V3 to be the last one, then PN=3. We are missing the PN information
>for V1 and V2 (PN should be 1 and 2 respectively), because we assign
>negative values to the PN of V1 and V2 and those negative numbers can only
>indicate there is more term to be read.
>Really appreciate your kind help!
>The AMBER Mail Reflector
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Received on Fri Mar 18 2005 - 23:53:00 PST
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