AMBER Archive (2009)

Subject: [AMBER] IDIVF and PN

From: s. Bill (s_bill36_at_yahoo.co.uk)
Date: Thu Jul 16 2009 - 07:11:27 CDT

Dear AMBER
If the author didn't specify the IDIVF factor in dihedral parameter in his paper, so should I assume it equal to one?
Also, in Amber file format, under dihedral section, it states that:
"The negative value of pn is used only for identifying the existence of the next term and only the absolute value of PN is kept." Sorry, what does "absolute value is kept" mean?
For example, in parm99
HC-CT-CM-CM   1    0.38        180.0            -3.         Junmei et al, 1999
HC-CT-CM-CM   1    1.15          0.0             1.         Junmei et al, 1999

what is the PN here for this dihedral bond?
thanks
bill

      
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