AMBER Archive (2002)

Subject: Dummy atoms...

From: Miguel de Federico (miguel_at_qorws1.uab.es)
Date: Wed Oct 23 2002 - 02:44:34 CDT

 I'm sorry I'm probably making an elementary question, but I was not
able to find an answer in the manual or the amber tutorials.

 I want to do a simple FEP calculation, in which there are some atoms
which disappear and therefore are converted into dummy atoms. I made the
prep file, and I also was able to save the unit (named c6x) without any
problem, with all properties for the perturbation included (as shown in
the tutorial). However, when I want to get the topology and coordinate
files, leap gives me an error message about the dummy.

 Here you have the last leap command and the error:

"
> saveamberparm c6x 20c6x.top 20c6c.crd
Checking Unit.
Building topology.
Building atom parameters.
For atom: .R<c6x 1>.A<D20 5> Could not find type: DH
Parameter file was not saved.
"

 How can I define the atom type for dummy atoms?

 Thank you in advance,

Miguel