Hi Users and Developers,
I recently noticed unexpected behavior with how tleap handles dihedral
parameters in in parm*.dat and frcmod files, and wanted to report it in
case it is helpful for someone else. Prior to Amber12, or so, dihedrals
were specified by the following format:
DI-DJ-DK-DL division kp PHI periodicity
Any additional strings at the end of the line were treated as comments.
Beginning with Amber12, the ability to set the 1-4 scaling values was
introduced, and an additional format became available:
DI-DJ-DK-DL division kp PHI periodicity SCEE=scee SCNB=scnb
However, it appears that a bug can develop in the current code
($AMBERHOME/AmberTools/src/leap/src/leap/amber.c) for certain
specifications of the dihedral. For example, if the following specification
is used:
OS-CG-OS-CG 1 0.55 300.0 -1.
2,2-Dimethoxypropane
... where "2,2-Dimethoxypropane" is intended to be a comment, the current
code sets the SCEE=2.0 because it reads the first number in the comment as
though it were setting the SCEE value. I confirmed that the following
specification works as intended:
OS-CG-OS-CG 1 0.55 300.0 -1. SCEE=1.2
SCNB=2.0 2,2-Dimethoxypropane
This doesn't appear to be a problem for any of the parm files distributed
with Amber, since those that don't specifically define SCEE/SCNB also don't
begin dihedral comments with numerals. I ran into this problem when using
files generated by another user who had only tested it on pre-Amber12
software.
I think a fix in $AMBERHOME/AmberTools/src/leap/src/leap/amber.c would be
not too difficult, but I don't have time at the moment to test it out. I
submitted a bug report on the bugzilla.
Best,
--Niel
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Received on Fri Oct 13 2017 - 12:30:01 PDT
