Re: AMBER: Question about Prep file

From: <>
Date: Fri, 22 Jul 2005 15:21:20 -0400
('binary' encoding is not supported, stored as-is) Using the *.dat file does solve that, thank you. The reason I used the
*.bin file was the following entry in the comments section when clicking
Dr. Baaden's name in the Amber parameter database. I mistook this to mean
that the *.bin file is the input file. Maybe a note could be made to
avoid future confusion by others?

Best Regards,


Amber parameters and input files

Marc Baaden

1. Prep files

1.1. Ions

Filename PDBS Comment
....................... ....................... ......................
H3O.bin H3O+.pdb Hydronium (+1)
Eu3+.bin EU3+.pdb Europium (3+)
Yb3+.bin YB3+.pdb Ytterbium (3+)
La3+.bin La3+.pdb Lanthanum (3+)
NO3.bin NO3-.pdb Nitrate (-)
PCL.bin PCL-.pdb Perchlorate (-)
TFL.bin TFL-.pdb Triflate (-)

==============Original message text===============
Hi Marc:

Actually, the basic Amber file formats have not changed since 4.1.
The original poster (ortiz) tried to feed the EU3+.bin file to LEaP, but
this is actually the *output* file from the old prep program, not its
input file. The input files needed are called PREPEU3+.DAT (and the
other *.DAT files you uploaded.) These are files that can be used as
input to prep, or to LEaP (using the loadAmberPrep command).

Thanks for contributing your parameters. I think if users know which files
are which, they won't have any problems, even with current versions of Amber.


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Received on Fri Jul 22 2005 - 20:53:01 PDT
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