[AMBER] tleap and sander minimization

From: Hegazy,Lamees <lamees.ufl.edu>
Date: Thu, 29 Jul 2010 14:35:45 -0400 (EDT)

Dear Amber users,

Iam preparing my protein for molecular dynamics simulations. In my
first step I used tleap to get the parameter and topology files
and the new pdb structure which I made from these files using
ambpdb command has completely different coordinates than the
original pdb structure.
The same happened with minimization using Sander. The resulting
minimized strucure has completely different coordinates than the
one I used before minimization. Are these issuea bugs in the
program or am I doing something wrong.

Sincerely,
Lamees 

--
Hegazy,Lamees
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Jul 29 2010 - 12:00:34 PDT
Custom Search