Dear Fabian,
If you just want to simulate the dynamics of the complex of DNA and cyclen-Cu(II)-H2O, as Marcelo suggested, MCPB.py can be used to parameterize the cyclen-Cu(II)-H2O first. There is an example about parameterizing an organometallic compound system using MCPB.py, which can be found in the SI of the MCPB.py paper: https://pubs.acs.org/doi/abs/10.1021/acs.jcim.5b00674 <https://pubs.acs.org/doi/abs/10.1021/acs.jcim.5b00674>.
If you want to study real catalysis of the system (breaking or forming chemical bonds), QM/MM simulation is necessary, but before you doing that you can use the classical molecular dynamics to equilibrate the system. And for generating the classical force field, you can use MCPB.py to parameterize the cyclen-Cu(II)-H2O complex as well.
Hope it helps,
Pengfei
> On Apr 6, 2019, at 12:56 AM, Fabian Glaser <fabian.glaser.gmail.com> wrote:
>
> Dear pengfei,
>
> No the ligand has not covalent bonds with the dna is the cyclen-Cu(II) -
> h2o system which i don't know how to treat.
>
> The copper is coordinated by the nitrogen's in the cyclen ring and the
> water, and it's key in the dna catalysis, i just want to study the Dynamics
> of the docked system for specific distances and angle that allow catalysis
>
> Thanks a lot
>
> Fabian
>
>
>
> On Sat, Mar 16, 2019, 17:19 Pengfei Li <ambermailpengfei.gmail.com> wrote:
>
>> Hi Fabian,
>>
>> For the Mg2+ ions, a nonbonded model is suggested due to the ionic nature
>> of Mg2+.
>>
>> For the Cu2+ ion, I am not sure I understand your question correctly or
>> not. So you have a cyclen-Cu(II) system as a ligand, and does this ligand
>> have covalent bond with the protein?
>>
>> -Pengfei
>>
>>> On Mar 12, 2019, at 10:00 AM, Fabian Glaser <fabian.glaser.gmail.com>
>> wrote:
>>>
>>> Dear amber experts,
>>>
>>> OK, so here comes one that may trivial for most, but not for me…
>>>
>>> I am willing to run MD for a protein gyrase, pdb 2xkk, which has four
>> MG+2 atoms in the catalytic center surrounded by water and asp acids. I
>> notice that in the advanced tutorial 20 there is a bonded and a non-bonded
>> model methodology, which one I should use for Mg+2 ??
>>>
>>> Additionally, to make things more complicated, I am using a
>> cyclen-Cu(II) system ligand based for docking on this target, which also I
>> would like to run MD on the docked complex, so I will need also to
>> parametrize the ligand Cu+2 bonded to this ligand. So the same question
>> here, how should I prepare the Cu+2 in this case??
>>>
>>> And comments, pointers or ideas or source of information will be more
>> than appreciated.
>>>
>>> Thanks in advance!
>>>
>>> Best,
>>>
>>> Fabian
>>>
>>> Fabian Glaser PhD
>>>
>>> Head of the Structural Bioinformatics section
>>> Bioinformatics Knowledge Unit - BKU
>>> The Lorry I. Lokey Interdisciplinary Center for Life Sciences and
>> Engineering
>>> Technion - Israel Institute of Technology, Haifa, Israel
>>> Web http://bku.technion.ac.il/
>>> Tel +972 (0) 4 8293701
>>>
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>>
>>
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Received on Sat Apr 06 2019 - 15:00:03 PDT
