AMBER Archive (2009)

Subject: Re: [AMBER] non standart residue library creation with tleap (Zn atom)

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Tue Nov 24 2009 - 12:09:45 CST

> Why I should gather or calculate prceise bond length and angle
> parameters if the PDB data already measured by X-ray analysis?

The equilibrium geometrical values that would ideally fulfill the
force field would likely be different from what is in the xtal
coordinates, which is the result of multiple terms added together.
In addition there are force constants to be determined which the
coordinates won't tell you. That said, you could probably estimate
the force constants by analogy with the existing ones, and use
the geometrical values for a 'quick and dirty' approach, which
may or may not satisfy reviewers. You might also want to read up
on force fields for ions specifically derived from multiple
xtal structures; sorry, I don't have references.

Bill

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