[AMBER-Developers] 1-4 Duplicate NB flagging when k atom index is one

From: Mark Williamson <mjw.sdsc.edu>
Date: Thu, 21 May 2009 21:33:14 +0100

Dear All,

Within the sections:


in a prmtop file, dihedrals are listed for a system being described. Each
dihedral is described using five numbers, the first four relate to the
indexes of the atoms in the dihedral and the fifth is a "pointer" into the
giving the associated parameters for that specific dihedral.

The first four numbers are not (as one would expect) the atom index (given
by the order in ATOM_NAME) of each atom in the dihedral, but instead the
atom index number minus one, multiplied by three.

For example, the dihedral listed in a prmtop as follows:

       0 12 18 24 2

would correspond to torsion 1-5-7-9 and point to number two in the
associated DIHEDRAL_* parameter lists.

AMBER denotes an IMPROPER torsion in its dihedral indexes by prefixing the
4th atom (l) with a negative sign. It does the same with the 3rd atom (k)
to indicate that the end group interactions (i.e. any 1-4 interactions) of
this torsion should be ignored.

My question is, what happens when k is atom one in the system and it needs
to be flagged to ignore its 1-4 contribution, e.g. :

Given a dihedral of atom index: 4-3-1-7

it becomes the prmtop'ed form of: 9 6 0 18

Here in lies the problem, you cannot put a sign on a zero:

9 6 -0 18

I'm currently hitting this with a sugar related test in the chamber code.
Any advice would be greatly received.



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Received on Fri May 22 2009 - 01:09:14 PDT
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