AMBER Archive (2008)

Subject: RE: AMBER: Tutorial 6

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Mon Jul 14 2008 - 13:48:05 CDT

Hi John,

 

Which tutorial 6 are you referring to here? I think maybe you mean this one:

 

http://www.rosswalker.co.uk/tutorials/psc_workshop/Tutorial_six/

 

If so then be aware that these tutorials are extremely old and are here
really only for historical reasons. You should really use the following set
of tutorials: http://www.ambermd.org/tutorials/

 

This tutorial was never designed to be used as an a standalone tutorial but
was part of a workshop hosted at the Pittsburgh Supercomputer Center. As
such parts of the tutorial may not make sense without the associated
lectures that go along with it.

 

As for the origin of those files I fear that has been lost in the sands of
time. Essentially they were just created from a pdb that described the
target structure - in the same way you'd generate a normal prmtop and inpcrd
file. If you open the prmtop and inpcrd files in something like VMD you will
be able to see what the structures are.

 

All the best

Ross

 

 

From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of
Beale, John
Sent: Monday, July 14, 2008 9:48 AM
To: amber_at_scripps.edu
Subject: AMBER: Tutorial 6

 

I am working through tutorial 6, the one that utilizes tazobactam and
beta-lactamase. I am at the point where I want to do targeted MD of the
tazobactam:beta-lactamase complex. There are two files that are referenced
and that can be downloaded. They are:

 

vm1_complex_target.prmtop

 

and

 

vm1_complex_target.inpcrd

 

 

There is no information in the tutorial about how these two target files
were generated. Can someone tell me what these files represent and where
they came from?

 

Thanks!

 

John

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
      to majordomo_at_scripps.edu