AMBER: questions on dummy atom types in FEP setup

From: Eric Hu <>
Date: Mon, 22 Nov 2004 13:37:54 -0800 (PST)

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.type
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:

dh 1.0 0.0
dc 12.0 0.0
dn 14.0 0.0
do 16.0 0.0




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


Do You Yahoo!?
Tired of spam? Yahoo! Mail has the best spam protection around
The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Mon Nov 22 2004 - 21:53:00 PST
Custom Search