Re: AMBER: Fwd: [chirality.c] Atom did not match

From: David A. Case <>
Date: Sat, 17 Nov 2007 08:53:01 -0800

On Sat, Nov 17, 2007, Francesco Pietra wrote:
> ATOM 50277 OH2 TIP3 307 47.752 43.891 17.330 1.00 0.00 W45 O
> ATOM 50278 H1 TIP3 307 46.913 43.577 17.668 1.00 0.00 W45 H
> ATOM 50279 H2 TIP3 307 48.403 43.284 17.681 1.00 0.00 W45 H


Atom names in an input pdb *must* match those in the library. For the
standard Amber water model, the residue name is "WAT", and the atom names are
"O", "H1" and "H2".

It may be obvious to a human (who is familiar with molecular modeling) that a
residue named "TIP3" is probably a water molecule, and that if one atom stats
with the letter "O", that is probably the oxygen atom.

But LEaP is restricted to examining the pdb file to see if there is an exact
match to something in a loaded library.


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Received on Sun Nov 18 2007 - 06:08:03 PST
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