AMBER Archive (2007)

Subject: Re: AMBER: working with Antechamber

From: Atila Iamarino (atila_at_usp.br)
Date: Wed Apr 11 2007 - 13:59:03 CDT

David Mobley wrote:
> Hi
>
>> 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. :)
>
> David
>
>> --
>> 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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>
I can't generate even the prepin file using pdb or the attached mol2 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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