AMBER Archive (2003)

Subject: AMBER: Basic potential question:

From: Wayne Dawson (dawson_at_nih.go.jp)
Date: Wed Dec 24 2003 - 09:56:37 CST

> can anybody tell me what are the potentials cff91,cvff,esff good
> for?(if they have some specific purpose) are they good RNA+proteins?

In all humility and due respect, they were certainly not good for
RNA. I think the Amber option is a far better choice if you are using
Discovery. If I remotely recall correctly in the Discover manual, I
think they say these potentials were mainly optimized for calculating
proteins, so _perhaps_ they work ok for most of the usual proteins
you'll find in PDB. In my own case, I did not find that they worked
all that well, but that may because of the type of proteins I had to
deal with.

The main problem in general with Discover is that it is largely a
"black box" to the user and therefore rather difficult to rip open and
see what is really inside --- particularly when you wonder why
something doesn't make much sense in a calculation.

...WD

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