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

From: vivek m <vivek.010484.gmail.com>
Date: Wed, 21 Dec 2016 23:47:57 +0530

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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> >>
> > <ZnO_cluster.png>_______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Wed Dec 21 2016 - 10:30:03 PST
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