Re: AMBER: Question about loadMol2

From: Thomas Steinbrecher <>
Date: Tue, 27 Mar 2007 13:24:55 -0700 (PDT)


>> I am having a problem with the loadMol2 command in xleap from Amber version
>> 9. Basically, when I try to load a molecule from a mol2 file (generated by
>> VMD), I get no errors but the unit is not created. So, whenever I do an
>> edit, desc, or check on my unit, xleap says my molecule doesn't exist.

just one suggestion, what I normally do when different programs do not
like structure files created by other ones is, use babel to read
it in and write it out again in the same format.

Babel is quite tolerant of format inaccuracies and normally gives files
that all amber programs will eat without complaining.

You can get babel at I think and all you would need to do

babel -imol2 <file> -omol2 <new_file>

Maybe that helps,


Dr. Thomas Steinbrecher
The Scripps Research Institute
10550 N. Torrey Pines Rd.
San Diego CA 92037, USA

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Received on Wed Mar 28 2007 - 06:07:45 PDT
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