[gmx-users] Reg: Your suggestions for Gromacs simulation using a cofactor and a Zn ion together

[Justin Lemkul]

On 10/4/19 7:53 AM, Amit Jaiswal wrote:
> Hello all,
>
> I am a novice in Gromacs and i wanted to do a simulation of a protein-zn-cofactor complex together. The problems raised during simulation are:
>
> 1. How can i position restrain Zn ion?

You shouldn't apply position restraints to the ion if the goal is simply 
to enforce proper coordination. You should use distance restraints or 
force field parameters that properly model Zn coordination without 
biasing potentials. If you need to restrain the ion simply during 
equilibration along with the protein, there are no special tricks here; 
just apply a restraint like any other atom (see the manual).

> 2. How can i generate a parameter file for NAD cofactor in Amber forcefield?

They already exist:

http://research.bmh.manchester.ac.uk/bryce/amber

You just need to convert the parameters to GROMACS format (see 
respective AMBER and GROMACS manuals for format) and write an .rtp entry.

> 3. What are the steps required to successfully run the simulation?

There's really no difference from any "normal" protein-in-water simulation.

-Justin

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Justin A. Lemkul, Ph.D.
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