GB protein simulation

From: Guanglei Cui <>
Date: Mon 19 Feb 2001 11:58:23 -0500

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

Guanglei Cui
Dept. of Chemistry
SUNY at Stony Brook
Stony Brook, NY 11790
Received on Mon Feb 19 2001 - 08:58:23 PST
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