AMBER Archive (2004)

Subject: Re: AMBER: problem with tleap in Amber

From: David A. Case (case_at_scripps.edu)
Date: Sun Feb 15 2004 - 23:10:31 CST

On Sun, Feb 15, 2004, donna j wrote:

> I tried running tleap on 1L1OC(that i extracted from the Protien Data
> Bank)...It has Zinc in it
> I got the following error
>
> FATAL: Atom .R<ZN 414>.A<ZN 1> does not have a type.

All residues in the pdb file have to be defined in LEaP before you use
the loadPdb command. If you have a residue that is ZN, you must define
a corresponding "unit" in LEaP. There is a lot of material in the mail
archives about getting parameters for zinc ions.

The plastocyanin tutorial describes one way in which a copper atom
could be incorporated into an Amber calculation. Something similar could
be done for zinc, or you could treat all of its interactions as nonbonded
interactions. There is more than one way to attack problems like these.

...good luck...dac 

-- 

==================================================================
David A. Case                     |  e-mail:      case_at_scripps.edu
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
10550 N. Torrey Pines Rd.         |  home page:                   
La Jolla CA 92037  USA            |    http://www.scripps.edu/case
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