[gmx-users] Creating metal ion dummy models for MD simulations.

[Abhishek Acharya]

Dear Mark,

Thanks for your reply.

I obtained the topology files from the  authors. Just for the record,
looking at the files, it is clear that they have parameterized the metal
ion as a single molecular entity with 7 atoms, arranged in an octahedral
configuration. Rest is quite straightforward and the details are all
available in the article.

I hope this info helps others in the user list.

Sincerely,
Abhishek


Abhishek Acharya
Research Associate,
Department of Molecular Nutrition
CSIR-Central Food Technological Research Institute,
Mysuru-570020

On Tue, Jul 25, 2017 at 10:50 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
> I suggest you contact the corresponding author of such papers and ask them
> to share, since a quick glance at their supporting information did not make
> clear to me what they had done.
>
> Mark
>
> On Tue, 25 Jul 2017 10:40 Abhishek Acharya <abhi117acharya at gmail.com>
> wrote:
>
> > Dear Users,
> >
> > I want simulate a protein bound to two copper ions. For this, I intend to
> > use a dummy model for the metal ions with 6 dummy atoms surrounding each
> > metal ion. The parameters will be obtained from the following
> publication:
> >
> > http://pubs.acs.org/doi/10.1021/acs.jpclett.5b01122
> >
> > Since, I am new to the use of dummy models in GROMACS, I wanted to know
> the
> > correct way to represent the topology for such models. I tried to look
> for
> > example .itp files but couldn't find one. I went though the gromacs
> manual,
> > especially dummy atoms section (or virtual sites). But, I am pretty sure
> > this is not applicable to my problem; virtual sites have no mass, whereas
> > the dummy models as described in the above publication have dummy atoms
> > with a mass of 3.000 amu. I am guessing that the correct way should be to
> > treat the dummy model as a single molecule with 7 atoms, one central
> metal
> > ion and 6 dummy atoms, but i may be wrong.
> >
> > Kindly let me know the correct method to represent the topology.
> > Alternatively, it would also be a great help if someone can provide itp
> > files used in the above study, or any example itp files with similar
> dummy
> > models.
> >
> > Also, which software is generally used to construct the coordinates for
> > such dummy models ?
> >
> > Thanks and Regards,
> >
> > Sincerely,
> > Abhishek Acharya
> > Department of Molecular Nutrition
> > CSIR-Central Food Technological Research Institute,
> > Mysuru-570020
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