-------- Original-Nachricht --------
> Datum: Thu, 23 Jul 2009 09:29:57 +0200
> Von: FyD <fyd.q4md-forcefieldtools.org>
> An: AMBER Mailing List <amber.ambermd.org>
> 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!
Oliver
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Jul 23 2009 - 10:07:05 PDT
