Re: [AMBER] Zinc Oxide and protein simulation with AMBER

From: Pengfei Li <ambermailpengfei.gmail.com>
Date: Thu, 22 Dec 2016 10:46:49 -0600

Hi Vivek,

You don’t need to use parmchk2 to generate related frcmod files due to in your system all the bond parameters can be generated using MCPB.py.

I have modified your PDB file and generated the mol2 files (see attached), in the PDB file, in order to make MCPB.py recognize the zinc ion, I have modified all the zinc ions to atom name ZN and residue name ZN.

You can use the PDB, mol2, and ZnO.in files attached to do MCPB.py modeling directly.

Kind regards,
Pengfei





> On Dec 21, 2016, at 12:17 PM, vivek m <vivek.010484.gmail.com> wrote:
>
> Hi Pengfei,
>
> I modified the input file as you suggested. But antechamber throws
> following error (but is able to complete). I truncated the errors for ease
> of reading.
> And parmchk2 gives error: "Atom type of Zn does not shown up in
> PARMCHK.DAT"
> I have attached the input structure for inspection.
> Please advice.
>
> =============antechamber error ============================
> For atom[1]:Zn1, the best APS is not zero, bonds involved by this atom are
> frozen
>
> For atom[2]:Zn2, the best APS is not zero, bonds involved by this atom are
> frozen
> ..
> ..
> ..
> For atom[6]:Zn6, the best APS is not zero, bonds involved by this atom are
> frozen
>
> For atom[7]:Zn7, the best APS is not zero, bonds involved by this atom are
> frozen
>
> For atom[8]:Zn8, the best APS is not zero, bonds involved by this atom are
> frozen
>
>
> For atom[23]:O11, the best APS is not zero, bonds involved by this atom are
> frozen
>
> For atom[24]:O12, the best APS is not zero, bonds involved by this atom are
> frozen
>
> ---Judge bond type for Residue 1 with ID of 1 and Name of ZNO ---
>
> ---Judge bond type for Residue 2 with ID of 2 and Name of ZNO ---
> ..
> ..
> ..
> ---Judge bond type for Residue 22 with ID of 22 and Name of ZNO ---
>
> ---Judge bond type for Residue 23 with ID of 23 and Name of ZNO ---
>
> ---Judge bond type for Residue 24 with ID of 24 and Name of ZNO ---
>
>
>
>
> On Wed, Dec 14, 2016 at 1:17 AM, Pengfei Li <ambermailpengfei.gmail.com>
> wrote:
>
>> Hi Vivek,
>>
>> You can check the SI of the MCPB.py paper: http://pubs.acs.org/doi/abs/
>> 10.1021/acs.jcim.5b00674 <http://pubs.acs.org/doi/abs/
>> 10.1021/acs.jcim.5b00674>. There is an example of metal organometallic
>> compound there.
>>
>> I guess MCPB.py can handle your case but the original PDB file for MCPB.py
>> modeling needs to have each zinc ion and each oxygen separated in different
>> residues (with different residue numbers).
>>
>> Let me know if you have other questions.
>>
>> Kind regards,
>> Pengfei
>>
>>> On Dec 13, 2016, at 11:50 AM, vivek m <vivek.010484.gmail.com> wrote:
>>>
>>> Thanks David.
>>> I read the manual. Followed the tutorial 20 of metal-proteins MD once
>> also.
>>> I am doubtful as my cluster is a cage like structure.
>>> I am attaching a image to make things clear.
>>> Please advice.
>>>
>>>
>>> On Tue, Dec 13, 2016 at 9:04 PM, David A Case <david.case.rutgers.edu>
>>> wrote:
>>>
>>>> On Tue, Dec 13, 2016, vivek m wrote:
>>>>>
>>>>> I want to perform molecular dynamics of (ZnO)12 cluster with a
>>>> protein.
>>>>> I have drawn the ZnO cluster and performed gaussian optimization to get
>>>> the
>>>>> correct geometry and charges. I have also performed docking of ZnO
>>>> cluster
>>>>> with my protein. I have also done the protein preparation as described
>> in
>>>>> the AMBER tutorials.
>>>>> I do not know how to move ahead from here. How do i prepare the ZnO-
>>>>> protein prmtop and inpcrd files.
>>>>
>>>> See sections 15.7 and 15.8 in the Amber 2016 Reference Manual.
>>>>
>>>> ...dac
>>>>
>>>>
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Received on Thu Dec 22 2016 - 09:00:03 PST
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