yep thanks I have already seen that tutorial!
So in principle it is not such trivial to preserve coordinates of the
ions within the pdb and apply tleap for the parametrizaion of whole
complex, is int? I asked because I wrote script for the preparation of
the amber input files while just looping the pdbs flom folder
consisted of different proteins so will be interested in most broad
sollution.
James
2016-04-27 13:07 GMT+02:00 Yigal Lahav <yigal.lahav.mail.huji.ac.il>:
> 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 - 06:00:08 PDT
