Re: mol2 file format in the future of amber

From: David A. Case <>
Date: Sun 22 Sep 2002 08:10:42 -0700

On Fri, Sep 20, 2002, M. L. Dodson wrote:

> I have seen sporadic references to the use of the mol2 file format in
> amber future development (in place of prep and frcmod files, IIRC).
> Would anyone be able to furnish a paragraph or so of explanation of how
> this would work? I do some special residue description development for
> my work, and would like to make sure the scripts, etc. I write will not
> need to be rewritten for the next version. For example, is there/will
> there be a "prep2mol2" program available (other than the capabilities
> built into antechamber or tleap)? Does this question even make sense?
> :-)

Basically, even in Amber7 one can use mol2 files for most things. You
have to use "mol2_to_off" to convert those to something LEaP can read;
the next version of LEaP will read mol2 files natively.

Antechamber can already read and write mol2 files, although there are some
minor glithces and annoyances that will be fixed up. In addition, antechamber
can convert prep to mol2 files already, so I don't see any need for a separate
"prep2mol2" program.

We will probably continue to support the "prepi" format, for backwards
compatibility, but I would prefer to retire that file format, since it is
not all that well documented, and it really offers nothing not available for

The "off" format will continue to be used for libraries in LEaP, and is needed
for free energy perturbation, where there is a need to store both the
perturbed and unperturbed atom types and charges.

..hope this helps...dac

David A. Case                     |  e-mail:
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:                   
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Received on Sun Sep 22 2002 - 08:10:42 PDT
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