Hi, I try to set up a FEP calculation by perturbing a
small organic
molecule to nothing in water and protein later.
However I keep getting
errors on the defined dummy atom types. Here is part
of the table using "edit selected atoms" from xleap.
Name Type Charge Element Unused
PERT.name PERT.type
Delta.charge
C01 c3 0.0244 C true
DC1 dc 0.000
H09 hn 0.1856 H true
DH9 dh 0.000
....
I use gaff atom types calculated by antechamber. The
frcmod file looks
like this:
MASS
dh 1.0 0.0
dc 12.0 0.0
dn 14.0 0.0
do 16.0 0.0
BOND
ANGLE
DIHE
Here is the error when I try to save the perturbed top
and crd files.
For atom: .R<ts1 0>.A<C01 1> type c3
Could not find perturbed type: dc
For atom: .R<ts1 0>.A<C02 2> type c3
Could not find perturbed type: dc
For atom: .R<ts1 0>.A<C04 4> type c3
Could not find perturbed type: dc
....
Eric
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Received on Mon Nov 22 2004 - 21:53:00 PST
