Hello everyone,
I've been combing through the prmtop and relevant potential parameters and
I've run across something that doesn't quite make sense to me. The improper
dihedral parameters are described in the amber format specification as:
IPT , JPT , KPT , LPT , IDIVF , PK , PHASE , PN
where IPT, JPT, KPT, LPT are the atoms, IDIVF is the division factor, PK the
barrier height (/2), PN the periodicity and PHASE is self-explanatory. My
problem primarily comes with IDIVF. In some frcmod files, like
all_modrna08.frcmod, there is no IDIVF number. frcmod.constph, however, has
a number "0" as the IDIVF factor, which should almost certainly cause a
divide-by-zero error if it was in fact a divisor (but it doesn't...). So my
question is this: is IDIVF just a holder? Is it meaningless in for an
IMPROPER since it will always be '1'? In that case, is "1" an appropriate
value to set IDIVF to in improper terms?
Thanks!
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Tue Aug 24 2010 - 12:30:06 PDT
