Re: [AMBER-Developers] sleap -> tleap migration

From: David A Case <>
Date: Fri, 18 May 2012 08:35:45 -0400

On Thu, May 17, 2012, Eric Pettersen wrote:

> systems are typically proteins or nucleic acids. For those, if tleap
> is provided a standard mol2 file with Sybyl atom types, e.g.:
> 1 N 49.6680 24.2480 10.4360 N.4 1 HIS1 0.0000
> then it will not know anything about the atom types...

I see. It should not be hard to add a variant of loadMol2 to have it act
like loadPdb, that is have it ignore the atom types in the input file and
look for a match in libraries that are already loaded.

For a moment, use loadPdb to read in coordinates for units that are
already known, and loadMol2, loadAmberPrep or loadOff to add a new unit
to the list of known ones. That is, loadMol2 is an alternative to
loadAmberPrep, not an alternative to loadPdb. [I'm not sure how sleap figures
out what to do....]


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Received on Fri May 18 2012 - 06:00:02 PDT
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