On Tue, Nov 6, 2012 at 9:32 AM, Fabian Glaser <fglaser.technion.ac.il>wrote:
> Hi all,
>
> I am new to amber so please forgive me if I ask trivial questions. I am
> looking to practice amber use for MD with proteins. I noticed there are
> many tutorials in the amber page, but many of them are outdated or not
> maintained.
>
The tutorials on
http://ambermd.org/tutorials are, in general, accurate.
The main "outdated" parts of the tutorials have to do with the choice of
force field.
Using the various simulation programs (e.g., sander, pmemd, etc.) does not
change from version to version (with one or two notable exceptions over the
past 5-10 years). New features are added, but existing functionality is
left unchanged unless it is not feasible to do that (the only thing I can
recall off the top of my head is scee and scnb being removed from the
&cntrl namelist in sander and pmemd). We also have a comprehensive test
suite to test existing functionality, making sure that results do not
change from version to version.
Therefore, even though some of the tutorials may have been developed 5-10
years ago, the sander/pmemd/tleap usage has not changed since that time.
The only things that have changed are force field names (e.g., ff94 ->
ff99 -> ff03 -> ff99SB -> ff10 -> ff12SB, etc.) and some various issues
that pop up from time to time.
The tutorials are designed to help demonstrate how to _use_ the various
programs, so updating the tutorials to consistently use the "latest" force
fields is a decidedly poor use of (very limited) time.
That being said, when parts of our tutorials *are* out of date, we are
unable to fix them unless they are reported.
So I suggest that you work through the tutorials on the Amber website, and
if you come to an impasse, report it so the tutorials can be updated (and
working through some of the force field/tleap issues will help you
understand that program better).
Good luck,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Wed Nov 07 2012 - 16:00:03 PST
