Re: amber-developers: Leap: atom types (hybridization)

From: David A. Case <>
Date: Tue, 1 Jan 2008 09:47:33 -0800

On Sat, Dec 29, 2007, Yong Duan wrote:
> We can of course change the code so such it aborts automatically whenever it
> finds an atom with undefined hybridization (or crash the computer ...).

I think it should re-format the hard disk first, then exit.

> Alternatively, which I happen to think is a sensible approach, the input
> coordinates should be used.

In your example, there aren't any "input coordinates" in the usual sense, but
there are the relations in the library description of the residue. I agree
that these should be preserved.

This is now entered in bugzilla:

> For those who want to see how does an amino acid with a flipped chirality
> look like, try,
> ************
> 1) remove those "addAtomTypes" from any of the leaprc.ffxx files
> 2) tleap -f leaprc.ffxx
> 3) aa=sequence{ACE ALA NME}
> 4) savepdb aa aa.pdb
> 5) quit
> ***********
> Put it on your favorite PDB viewer.

Received on Wed Jan 02 2008 - 06:07:25 PST
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