Hi James,
I recommend you use the Metal Center Parameter Builder ( MCPB.py )
http://ambermd.org/tutorials/advanced/tutorial20/
I used it for modeling chlorophyll.
Good luck,
Yigal.
On Wed, Apr 27, 2016 at 12:25 PM, James Starlight <jmsstarlight.gmail.com>
wrote:
> Dear Amber users!
>
> I am interesting in param set which should I use in tleap input file
> for proper recognition within given PDB of some buried metalo-binding
> cofactors (not covalently bound to the polypeptide chain) like in case
> of Cythochrome-C (HEM with Fe).
>
> Also could someone recommend me simple preparation workflow for any of
> Metal-binding proteins (even without of additional cofactors like
> Calmodulin). E.g typically I use pdb2pqr to prepare PDB prior to the
> tleap parametrization which is unfortunately remove all ions from the
> initial pdb. Is it method to present it within buried protein sites
> and parametrize properly using some amber param-set?
>
> Thanks for help!
>
>
> James
>
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Received on Wed Apr 27 2016 - 04:30:04 PDT
