Re: AMBER: RED-vIII fails

From: FyD <>
Date: Tue, 30 Oct 2007 22:38:03 +0100

Quoting Jesper Soerensen <>:

> Files are attached, I figured I'd include all the data, as the file size
> wasn't too different.

- 1st in the tutorial, it is written
in the introduction:
"RESP was recompiled using qtol = 0.1d-5, maxq = 5000, maxlgr = 500
and maxmol = 200"
You are using a two molecules RESP fit; with for the 1st molecule (2
conformations x 4 orientations) and for the 2nd molecule (1
conformation x 4 orientations). Thus, your charge derivation start to
complex; I would recompile RESP with the keywords provided to avoid
additional error messages...

- Then, in,
the INTER-MCC are defined between a molecule 1 & a molecule 2 (only).
The molecule 1 being the donor of chemical group and the molecule 2
the acceptor of chemical group. In your example, you inverted the
molecule 1 and 2 and used the molecule 2 as a donor of chemical group.
Try to switch the order of the molecule, and see how it works: It
should be OK.
I want to underline that the way INTER-MCC have been set up in
R.E.D.-III is quite rigid. In particular, R.E.D.-III only allows to
build molecular fragments as defined in Cieplak et al. J. Comput.
Chem., 1995, 16, 1357-1377. We changed that in R.E.D. IV and the
building of more complex force field topology databases is now
possible (and the way to do it is really less rigid).

- Finally, once you will have generated the Tripos mol2 file for your
terminal fragment you might considering reading We just put new
versions of the LEaP files to be downloaded.

Please, tell me if this solves your problem...

regards, Francois

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Received on Wed Oct 31 2007 - 06:08:07 PDT
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