Re: [AMBER] MM PBSA tutorial

From: Jason Swails <>
Date: Thu, 28 Mar 2013 09:37:04 -0400

In addition to Thomas's email, I'll add a couple comments. Learning how to
use Amber will take time. It is important not to treat any program in
Amber as a black box (that is, you should know what the program is doing)
-- this is especially true for MM/PBSA analyses. You should know how to
run MM/PBSA calculations without using a script before using the script to

The amount of time learning Amber requires depends on how much experience
you have with the general computational chemistry environment in the first

Do you know UNIX and the command-line? If not, start there: -- the first few chapters should
be enough to get you started using a terminal.
Do you know computer simulation and molecular dynamics/molecular mechanics?
 If not, pick up some kind of introductory text (e.g., Chris Cramer's or
Andrew Leach's books) and go through the introductory chapters there.

You've already said you're new to Amber. Look at for
information about downloading the latest version of AmberTools (the manual
is included in amber12/doc/AmberTools12.pdf). Install Amber (there are
good online resources with links on the Amber web site and instructions in
the manual).

Then work through some of the basic tutorials -- start from the beginning
and work through the first 2 or 3. (You will need a valid Amber license to
run the molecular dynamics simulations).

Google is really your friend here. If you get an error message that you
can't figure out, paste it into google and search. People on the list
responding to emails are more likely to spend their time helping people
that attempt to help themselves. The time that you spend learning the
source of your own errors will greatly help you up the learning curve.

In any case, running MM/PBSA calculations 'right now' is a poor strategy --
you should build a solid foundation before attempting real simulations (a
process that should take several weeks in my experience).

If and when you do have to ask questions to this list because you can't
figure them out yourself, the way you ask the question is important. This
link does a good job of describing how to ask a good question, IMO:

Good luck,

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
AMBER mailing list
Received on Thu Mar 28 2013 - 07:00:03 PDT
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