Re: AMBER: working with Antechamber

From: David Mobley <>
Date: Wed, 11 Apr 2007 11:34:55 -0700


> I'm trying to generate topology files for ritonavir, a HIV1 protease
> inhibitor, following the Efavirenz tutorial. I don't know which Force
> field I should use. Using either xleap or PRODRG server antechamber
> crashes and doesn't understand the bonds.
> Attached are the files from xleap and prodrg
> Thanks,

What step of the tutorial are you at? If you are trying to feed the
attached pdb file into xleap, of course it won't work, because for
small molecules xleap needs a mol2 file or a prepin file and a frcmod
file, NOT a pdb file. That's why the tutorial has you prepare a prepin
file. :)


> --
> Atila Iamarino
> L.E.M.B. - Laboratory of Molecular Evolution and Bioinformatics
> Av. Prof. Lineu Prestes, 1734 - USP (University of São Paulo) - ICB
> Zip: 05508-000 Phone: +55 11 30917290 / +55 11 30918453
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Received on Sun Apr 15 2007 - 06:07:09 PDT
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