Hi Martin,
Here is some information I found on the format description page of the Amber
website (
http://amber.scripps.edu/formats.html). Hopefully this is helpful
to you.
NOTE: the atom numbers in the following arrays that describe bonds, angles,
and dihedrals are coordinate array indexes for runtime speed. The true atom
number equals the absolute value of the number divided by three, plus one.
In the case of the dihedrals, if the fourth atom is negative, this implies
that the dihedral is an improper. If the third atom is negative, this
implies that the end group interations are to be ignored. End group
interactions are ignored, for example, in dihedrals of various ring systems
(to prevent double counting of 1-4 interactions) and in multiterm dihedrals.
-----Original Message-----
From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf Of
Martin Stennett
Sent: Thursday, August 30, 2007 4:36 AM
To: amber.scripps.edu
Subject: AMBER: Dihedrals in Sander
Hi,
I've been looking through some of the prmtop files created in my system
and some of the dihedral pointers are negative, the first place I found
the dihedrals used is in ene.f and in this intance the sign of the
pointer is discarded. What purpose does the sign serve?
Regards,
Martin Stennett
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Received on Sun Sep 09 2007 - 06:07:21 PDT
