Hi James,
> On Apr 27, 2016, at 10:01 AM, James Starlight <jmsstarlight.gmail.com> wrote:
>
> 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?
>
For the situations where the coordinate bonds are not specified in the input prep/mol2 file, you need to use the bond command in tleap to specify these coordination bonds.
> 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?
To my knowledge there is no software to do this kind of work specifically in AmberTools.
Other options would be like H++, which is a web-server to add hydrogens, but it also deletes the water, ion, and non-standard residues during the process. But in the end you could get Amber topology and coordinate files (without water, ion, or non-standard residues), and using ambpdb software you can create the PDB file which has amber-like residue and atom names. Then you can add the water, ion, and non-standard residues to the new PDB file from the former PDB file manually. In the end you can have a PDB file for use in tleap modeling.
Kind regards,
Pengfei
>
> 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 Thu Apr 28 2016 - 08:00:03 PDT
