AMBER Archive (2005)

Subject: Re: AMBER: Question about Prep file

From: opitz_at_che.udel.edu
Date: Fri Jul 22 2005 - 14:21:20 CDT

('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,

Armin

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.

...regards...dac

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