Re: Questions on crosslinking residues

From: David A. Case <>
Date: Thu 3 Oct 2002 08:04:18 -0700

On Thu, Oct 03, 2002, Nicholson, James D Mr ARO wrote:

> I was concerned about assigning charges and new bond parameters for some of
> these atoms. However, I'll give it a try with the assymetric pieces and
> hope that leap ignores the fact that the atoms in the templates aren't
> bonded correctly for their specified atom types. So, my concern was that I
> would be fighting leap over what charges and bond/angle/torsion parameters
> were assigned.

I'd suggest using antechamber (or something) to get a proper template.
It sounds like you are expecting way too much intelligence to LEaP. It
considers the template to be correct. If the atom types in the template
aren't what you want, you need to fix that before running LEaP. LEaP
simply lines up atom names in the pdb with those in the corresponding
residue in the library, and assigns the coordinates from the pdb file to
those atoms. *You* (not LEaP) should be deciding all issues concerning
charges and parameters.


David A. Case                     |  e-mail:
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
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Received on Thu Oct 03 2002 - 08:04:18 PDT
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