AMBER Archive (2005)Subject: AMBER: question about periodicity of torsion parameter
From: jz7_at_duke.edu
Date: Fri Mar 18 2005  16:08:50 CST
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!

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