[gmx-users] Simulation of aggregated proteins

[Mark Abraham]

Hi,

Judicious reading of the documentation will show that you can get pdb2gmx
to consider TER and chain ID changes as breaking molecules, or not. But if
there are pdb model fields then you need input that does not use them any
more.

Mark

On Fri, Dec 22, 2017, 8:11 PM João Henriques <joao.m.a.henriques at gmail.com>
wrote:

> If the PDB has each protein with separate chain entries (A, B, etc) then
> this shouldn't be a problem. pdb2gmx will produce separate topologies for
> each chain and an overall topology that reads from each of the individual
> topologies and contains the other directives about FF, water model, posre,
> etc.
>
> J
>
> On Fri, Dec 22, 2017 at 9:29 AM, RAHUL SURESH <drrahulsuresh at gmail.com>
> wrote:
>
> > Dear all
> >
> > I have a PDB entry having 10 models(Aggregated structure). Here I want to
> > carry out the molecular dynamic simulation as such in aggregated form.
> But
> > gromacs is considering only one model in the PDB structure. How can I
> > simulate it as a whole.?
> >
> > Thank you
> >
> > --
> > *Regards,*
> > *Rahul Suresh*
> > *Research Scholar*
> > *Bharathiar University*
> > *Coimbatore*
> > --
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