AMBER Archive (2002)

Subject: Re: Interface and Amber 7.0

From: David Pearlman (dap_at_vpharm.com)
Date: Tue Aug 27 2002 - 11:35:19 CDT

Actually, this is not entirely correct.

A) Interface was included with the Amber6 distribution.

B) Interface6 works with Sander6, Sander_Classic6 and Gibbs6.

C) Interface6 should work with Gibbs7 since Gibbs7 should have the
   same input as Gibbs6.

D) Sander_Classic is not in the Amber7 distribution. The functionality
   of Sander_Classic is not all in the version of Sander that is
   included with Amber7. If you need Sander_Classic functionality (or
   if the functionality of Sander_Classic is sufficient), use
   Interface6 with Sander_Classic6.

E) I am not sure what differences have been made to the input of
   Sander7 versus Sander6, so I can't say what changes might need
   to be made to Interface to use it with Sander7, but they aren't likely
   to be that "difficult".

F) The Interface input is easily extensible to include additional
   variables in more recent versions of code by using the "Set" command.
   E.g.

   set new_variable_name = value

   will add a namelist definition for new_variable_name and give it the
   supplied value. This can be used to extend the interface front end
   if you add new variables.

dap

"David A. Case" wrote:
>
> On Mon, Aug 26, 2002, Nigel D Priestley wrote:
> >
> > Apologies if this is a question covered under RTFM. We recently upgraded
> > from Amber5.0 to Amber7.0 and there is no trace of the Interface program
> > on the CD we received. Interface from 5.0 doesn't seem to be compatible
> > with Amber7.0. Did we miss something somewhere?
>
> No, you didn't miss anything. Interface was never updated for Amber 7.
> Basically, no one volunteered to do the (difficult) task of keeping both the
> program and a second manual (for ambint) in "sync" with sander and its
> manual.
>
> You should be able (I think) to use interface 5.0 with gibbs 7.0, since that
> program has changed very little.
>
> ..regards....dac
>
> --
>
> ==================================================================
> David A. Case | e-mail: case_at_scripps.edu
> Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896
> The Scripps Research Institute | phone: +1-858-784-9768
> 10550 N. Torrey Pines Rd. | home page:
> La Jolla CA 92037 USA | http://www.scripps.edu/case
> ==================================================================