From: Leonardo Sepulveda Durán (leonardosepulveda_at_gmail.com)
Date: Thu Jun 09 2005 - 16:42:15 CDT
Did you assembled collagen in a hexagonal close packing structure....
Are you meaning that your protein is the result of a docking of a lot
of collagen segments????? maybe that is the problem. Check with vmd if
vdw radii of diferent chains have clashes. And using PBC would be a
better option to solvate a long molecule as collagen... The other
clue: minimize solvent first and maintain structure fixed with atom
forces off, maybe that will help to know if the problem comes from the
protein or from the solvent...And other thing... How many atoms does
your system have ????
On 6/9/05, shgnwgn_at_eden.rutgers.edu <shgnwgn_at_eden.rutgers.edu> wrote:
> The energy is so high that it reads 99999999.99999 from the very
> beggining. nothing else has energy lower enough to lower the total energy
> value over a 100 ps cycle. the program does not crash.
> i got the 1qsu collagen molecule from <rcsb.org>
> i assembled the collagen in a hexagonal close packing crystal structure,
> with 1qsu in hyperchem6. I then added hydrogen and water sphere in vmd.
> > 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
> > ones???
> > and What part of the structure you prepared with hyperchem????
> > Leonardo
> > 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.
> >> ken
> > ~~~~~~~~~~~~~~~~~~~~~~~~~
> > Leonardo Andres Sepúlveda Durán
> > Graduado de Bioquimica
> > Universidad de Chile
> > ~~~~~~~~~~~~~~~~~~~~~~~~~
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