Re: AMBER: Question about Prep file

From: David A. Case <>
Date: Fri, 22 Jul 2005 11:34:57 -0700

On Fri, Jul 22, 2005, Marc Baaden wrote:
> the parameters, prepfiles etc. for the lanthanides (and related calixarene
> ones) were used with an older Amber version (v4.1). I just checked, and they
> still do work with my older amber executables, but require the
> prep-link-edit-parm sequence that was used at the time.
> Unfortunately I am not certain about how you would need to go about
> converting them to the current Amber 8 format, or whether there are some
> specific options for backwards-compatibility built into Leap.
> But in any case I think you brought up an interesting question: what should
> one do to keep previous work still usable with current amber versions ? Are
> there any guidelines about how to convert not only topologies but also input
> files. Maybe some of the Amber developers could give us some precious hints?

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 - 19:53:00 PDT
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