Dear All,
Within the sections:
DIHEDRALS_INC_HYDROGEN
DIHEDRALS_WITHOUT_HYDROGEN
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
DIHEDRAL_FORCE_CONSTANT, DIHEDRAL_PERIODICITY and DIHEDRAL_PHASE lists
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:
%FLAG DIHEDRALS_WITHOUT_HYDROGEN
%FORMAT(10i8)
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.
regards,
Mark
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Received on Fri May 22 2009 - 01:09:14 PDT
