AMBER Archive (2006)

Subject: AMBER: 1st 2 lines of restart files

From: hayden (s0237717_at_sms.ed.ac.uk)
Date: Thu May 25 2006 - 06:40:03 CDT

Dear Amber users

I am currently developing some code for doing various manipulations of
protein coordinates. This inevitably means I need to create restart files on
the fly. My current strategy has been to generate coordinates and velocity
values in an amber format and then append them to a standard file that
contains 2 lines of a usual restart file. However, I have noticed that the
first 2 lines of the restart file are not superfluous, and that my choice of
these first 2 lines affect drastically the nature of my dynamics.

Consider the first few lines of a restart file below:

&SP

   60 0.8001000E+01
   3.7126232 5.4046935 -0.6650335 3.6504821 4.4052897 -0.5330020
   4.8881885 6.0726386 -0.0402767 5.2856881 6.8288725 -0.7171849
   4.2857077 6.7669687 1.2096267 3.3414002 7.2507716 0.9599908

The first line appears to indicate the first residue in the sequence (this
is fine I take this into account when creating the restart file). The second
line begins with the no. of atoms being considered (this is no problem
either). However, the third piece of information is not obvious, and it's
value appears to affect the energies of the system when I restart sander.

My Question is: What does this "third piece" of information indicate?

Many thanks

Hayden
______________________________________________
Hayden Eastwood
Perdita Barran Research Group
Joseph Black Building
Edinburgh University
West Mains Road
EH9 3JJ
 
Tel: 0131 650 4773
e-mail: s0237717_at_sms.ed.ac.uk
Research page:http://homepages.ed.ac.uk/pbarran/PBRG/
"You have to be an academic to believe some things; no ordinary person would
be so stupid." -George Orwell

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu