AMBER Archive (2005)

Subject: Re: AMBER: tleap load pdb file

From: David A. Case (case_at_scripps.edu)
Date: Fri Feb 04 2005 - 10:35:49 CST

On Fri, Feb 04, 2005, xiaowen wrote:

> Amber8 is installed on IBM-AIX unix computer.

> Dr. Ross help me to check the input pdb files,
> works fine on his computer.
>
> > test1=loadpdb nuc.pdb
>
> Loading PDB file: ./nuc.pdb
> (starting new molecule for chain T)
> -- residue 536870912: duplicate [] atoms (total 438)

If the above is really true (i.e. that the input pdb file used here worked for
Bill), then someone with access to a machine like yours will have to volunteer
to look at this problem. But I would still think you should check some things
yourself:

1. double-check that the test.leap test suite works on your IBM computer; you
say that you ran the tutorials, so I am assuming that most aspects of LEaP are
working fine for your setup.

2. try to make a smaller version of nuc.pdb, to see if that will work.
Is there actually a chainid "T" in the input? How many atoms does it have?

...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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