The overall charge of the ligand is zero, and I am using explicit solvent.
I here is a snippet of my perturbation file:
....
set lig.4.1 pert true
set lig.4.2 pert true
....
set lig.4.1 pertName C1
set lig.4.1 pertType CG
set lig.4.1 pertCharge -0.0410
set lig.4.2 pertName H1
set lig.4.2 pertType H2
set lig.4.2 pertCharge 0.0000
....
solvatebox lig TIP3PBOX 8
saveamberparmpert lig abc_inwat.top abc_inwat.crd
Looks like the "charge" command reads the input after pertCharge as Qs,
not deltaQs. This input format was adopted from AMBER8 and later versions,
but the "charge" routine has not been modified accordingly.
Thanks,
austin-
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Received on Wed Jan 31 2007 - 06:07:42 PST
