[gmx-users] DNA-Protein complex

[aayattimg at bose.res.in]

> I think you don`t need to build topology separately. Using appropriate
force field will do. For protein-DNA simulation amber99sb works well.
Amber99bsc1.ff is a new module available for gromacs users. You may use
them or it is always better to refer literature to use the more
appropriate forcefeild.
Good Luck!
Check the literature to see what others that are simulating similar
> molecules are using and looking to study similar "things" (energies,
> structures etc) that you are.
>
> Catch ya,
>
> Dr. Dallas Warren
> Drug Delivery, Disposition and Dynamics
> Monash Institute of Pharmaceutical Sciences, Monash University
> 381 Royal Parade, Parkville VIC 3052
> dallas.warren at monash.edu
> ---------------------------------
> When the only tool you own is a hammer, every problem begins to resemble a
> nail.
>
>
> On Wed, 29 Jan 2020 at 00:53, Rakesh Bhowmick <inforak.007 at gmail.com>
> wrote:
>
>> I am new in the field of molecular dynamics and simulation. I am trying
>> to
>> learn online tutorial for gromacs. I have docked my DNA with protein in
>> HADDOCK. I want to run a simulation in gromacs. Can I make topology file
>> of
>> the complex together or I need to make topology file separately. Which
>> forcefield should I use for DNA protein complex?
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