[gmx-users] Simulation of aggregated proteins

João Henriques joao.m.a.henriques at gmail.com
Fri Dec 22 10:09:28 CET 2017

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,


On Fri, Dec 22, 2017 at 9:29 AM, RAHUL SURESH <drrahulsuresh at gmail.com>

> 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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