Yes, these should be available when you install Ambertools 1.5 under
$AMBERHOME/dat/mtkpp/ZAFF/
If you want to generate frcmod and prep files from these XML files, then use
a bcl input like the following(change $AMBERHOME to your path) and run MCPB
on it.
loadParam $AMBERHOME/dat/mtkpp/parm94.xml
loadParam $AMBERHOME/dat/mtkpp/parm_gaff.xml
loadParam $AMBERHOME/dat/mtkpp/metals/metalParm.xml
loadParam $AMBERHOME/dat/mtkpp/ZAFF/ZAFF_parm.xml
writeFrcmodFile ZAFF.frcmod ZAFF
loadLib $AMBERHOME/dat/mtkpp/ZAFF/ZAFF.xml
writePrepFile ZAFF.prep Zn-CCCC
quit
On Sun, Jul 17, 2011 at 10:52 AM, <moitrayee.mbu.iisc.ernet.in> wrote:
> Dear Amber Users,
>
> I am trying to simulate a zinc containing enzyme with CCCC and CCCH
> tetrahedron
> coordination. I have read the paper on MCPB and also the manual with
> AmberTools1.5. The paper mentions that such a FF calculation has been
> already
> done for the coordinations of my requirement. Are these FF available for
> the
> users of AMBER or do we have to repeat the example shown for 1AMP in the
> manual
> for the system of our choice?
>
> Any suggestion in this regard would be of great help.
>
> Thanks a lot in advance.
>
> Best Regards,
> Moitrayee
>
>
> --
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>
>
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Received on Fri Aug 26 2011 - 07:30:02 PDT
