Hi,
Two issues tripped me up recently with regards to MDL format. I wonder if
we could clarify them in the AMBER manual.
First:
The "CHG" Flag says:
%FLAG CHG
%FORMAT(5e16.8)
REAL*8(NSITE) Partial charge for each solvent site (e).
But I believe it has to be multiplied by 18.2223.
Also,
%FLAG LJSIGMA
%FORMAT(5e16.8)
REAL*8(NSITE) Lennard-Jones rmin/2(σ ∗/2) for each solvent site (Å). Note
that this is not σ .
Can we rename this variable? Maybe LJRMIN. You could see how this could
cause problems.
-Dan
--
Dr. Daniel J. Sindhikara
Institute for Molecular Science
E-mail: sindhikara.gmail.com
Website: http://sites.google.com/site/dansindhikara/
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Received on Mon Dec 12 2011 - 04:00:02 PST
