From: Leonardo Sepulveda Durán (leonardosepulveda_at_gmail.com)
Date: Thu Jun 09 2005 - 14:50:31 CDT
MMM....it sounds like your initial structure have some serious atom
overlapping...But anyway , is difficult to say anything about the
issue because data you give is insufficient. ¿When the energy becomes
very high? During minimization or dynamics??? does the program
crashes? what happens with total energy??? sometimes vdw energy
increases during minimization but electrostatic goes down giving an
overall energy decrease, (sometimes I have seen it with when I have
use a minimization with solvent fixed)
But as i said first, this sound like atomic clashes due to a bad
system preparation protocol.
How did you create your psf and pdb? with Vmd ??? added waters are in
a different segment than cristallographic?? can you see in vmd if your
preparation method have supperpose Crisytallographic waters with added
and What part of the structure you prepared with hyperchem????
On 6/9/05, shgnwgn_at_eden.rutgers.edu <shgnwgn_at_eden.rutgers.edu> wrote:
> i have a structure made of 11 helixes of collagen. when i run the
> minimization and equilibration of the structure in a water sphere, without
> the water molecules from the protein data bank, the program runs fine.
> however, when i include the water molecules, the vanderwalls energy values
> are too large. it actually is so large the program can't calculate to
> it's decimal.
> i made the structure with hyperchem 6, if it makes a difference.
> i would appreciate any advice, since my research focuses on the effects of
> the structural water from the protein data bank.
Leonardo Andres Sepúlveda Durán
Graduado de Bioquimica
Universidad de Chile
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