AMBER Archive (2001)

Subject: GB protein simulation

From: Guanglei Cui (cuigl_at_morita.chem.sunysb.edu)
Date: Mon Feb 19 2001 - 10:58:23 CST

Dear Amber Users,
   I've been having trouble with GB protein simulations. The explicit
solvent simulation shows the initial structure of a 43-residue protein is
really stable with a RMS deviation around 1.5A on average. However, the GB
simulations I did show large deviation after a while no matter whether it's
constant energy or constant temperature regime in the production run (I use
constant temperature in equilibration dynamics all the time). I'm using
saltcon = 0.2, cut = 99 and offset = 0.09. I'm not sure whether the saltcon
is appropriate for this system because there're quite a few charged
sidechains in the protein. I wonder if anyone has successfully reproduced
the result of explicit solvent dynamics for a protein in a long dynamics
(say above 10ns). I'll be really grateful if someone can shine some light on
me.

Guanglei Cui
Dept. of Chemistry
SUNY at Stony Brook
Stony Brook, NY 11790