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

[Mark Abraham]

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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