AMBER Archive (2009)

Subject: Re: [AMBER] saquinavir parameterization with antechamber

From: Oliver Kuhn (
Date: Thu Jul 23 2009 - 03:06:00 CDT

-------- Original-Nachricht --------
> Datum: Thu, 23 Jul 2009 09:29:57 +0200
> Von: FyD <>
> An: AMBER Mailing List <>
> Betreff: Re: [AMBER] saquinavir parameterization with antechamber

> Oliver,
> > After adding hydrogens with open babel, divcon runs a long time (and
> > doesn't stop). When I switch to resp charges, its the same.
> > How long should a resp or am1 calculation take for my molecule?
> Did you check the hydrogens you added & do you agree with what was
> automatically built ?
> am1 calculations should be quick; resp fit is usually very quickly done.
> may be others have comments here about divcon.
> regards, Francois

I got this from the amber mailing list and it worked. I will have to check what the parameters are and what they change. The input was from the Dundee prodrg server but I think it will work with any mol2 file if there are hydrogens :-)

antechamber -i lig.mol2 -fi mol2 -o lig.prepin -fo prepi -c bcc -s 2 -mk "CARTESIAN AM1 STANDARD DIRECT OPT=BFGS XTEST=0.0001 MAXOPT=20000"
$AMBERHOME/exe/parmchk -i lig.prepin -f prepin -o lig.frcmod

Thanks for your help!

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