AMBER Archive (2005)

Subject: Re: AMBER: question about periodicity of torsion parameter

From: Carlos Simmerling (carlos_at_ilion.bio.sunysb.edu)
Date: Fri Mar 18 2005 - 16:51:40 CST

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

===================================================================
Carlos L. Simmerling, Ph.D.
Associate Professor Phone: (631) 632-1336
Center for Structural Biology Fax: (631) 632-1555
Stony Brook University Web: http://comp.chem.sunysb.edu/carlos
Stony Brook, NY 11794-5115 E-mail: carlos.simmerling_at_stonybrook.edu
===================================================================

jz7_at_duke.edu 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
>To post, send mail to amber_at_scripps.edu
>To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
>
>
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu