Dummy atoms...

From: Miguel de Federico <miguel_at_qorws1.uab.es>
Date: Wed 23 Oct 2002 09:44:34 +0200

 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,

Received on Wed Oct 23 2002 - 00:44:34 PDT
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