Re: [AMBER] Simulation with Protein, cofactor and Ligand

From: David A Case <>
Date: Wed, 1 May 2019 13:53:53 -0400

On Fri, Apr 26, 2019, Prasanth G, Research Scholar wrote:
>I am interested in carrying out an amber simulation with protein along with
>a cofactor, Glutathione ( C10 H17 N3 O6 S) and a ligand.
>Could you please, let me know, if there is any protocol to be followed for
>this kind of simulation.
>In my humble opinion,
>we need to-
>1) use antechamber and make the topology and coordinate files for both
>cofactor and the ligand
>2) prepare protein using H++ server
>3) combine all the three into a complex using tleap
>4) carry simulation.

Above sounds correct.

>My question is, do we need to use any special restraints for the cofactor?

No: a "cofactor" is just a ligand by another name....

Of course, if you have a good starting structure, one generally wants to
restrain the parts you know to their initial coordinates during the
equilibration phase, gradually removing such restraints as you proceed.

...good luck....dac

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Received on Wed May 01 2019 - 11:00:03 PDT
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