Yep, right thanks!
And coordination bonds between metalls also will not be present in the
final system if we just parametrize the whole system simply using
tleap, no?
BTW the question- how to preserve all atoms from the initial pdbs
changing atom names to amber-like? E,g I am using pdb2pqr
pre-processing of the pdb to amber and by the end it delete everything
but not protein.
Are there another software e.g from amber-tools which will be better
to use instead of pdb2pqr?
Thanks!
J.
2016-04-27 15:53 GMT+02:00 Pengfei Li <ambermailpengfei.gmail.com>:
> Hi James,
>
>> On Apr 27, 2016, at 8:54 AM, James Starlight <jmsstarlight.gmail.com> wrote:
>>
>> 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
>
> To my knowledge, tleap could just perform modeling and could not perform parameterizations itself. You can preserve the atomic ions in PDB file when modeling related system using tleap due to Amber has library file for atomic ions (atomic_ions.lib in recent versions). However, for the HEME group, Amber doesn’t have standard lib file in its database, you can use the files from here: http://sites.pharmacy.manchester.ac.uk/bryce/amber <http://sites.pharmacy.manchester.ac.uk/bryce/amber>, or you can parameterize the system by using MCPB.py.
>
> Kind regards,
> Pengfei
>
>>
>> 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 - 07:30:02 PDT
