> Furthermore, the residues around are displaced which
> they are not supposed to do - I have included low vdw radii and the bonding
> energy has a very high force constant (100 ) - can I get the clashing part
> of Gmax out?
The atom indicated by GMAX is the one to focus on.
What is it? What type? What vdw params? What bonded to?
Are you expecting that a high bonding force constant will somehow
compensate for low vdw radii? That would only work in a highly
constrained system, likely with just a few atoms that could not
form vdw contacts.
> When I look in the pdb it seems fine so there is a clash I am
> not able to see.
The clash probably develops as atoms are pulled together.
If you print crds for every step of md or min, you likely will
see the problem developing.
Bill
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Received on Tue Jul 27 2010 - 12:00:04 PDT
