[gmx-users] Simulation of Protein-Protein Complex

[Justin Lemkul]

Please keep the discussion on the mailing list.

On 4/2/20 3:38 PM, Surya Sanjay wrote:
> Hello Dr. Lemkul,
> You were very helpful (I was pondering this problem for about four 
> days before you told me this and it all makes sense now). To complete 
> the solvation step, should I combine the topol.top files of both 
> protein chains?

You should only ever have one topol.top. pdb2gmx will write each protein 
chain topology to .itp files that are #included within it.

-Justin

> Thanks,
> Surya
>
> On Thu, Apr 2, 2020 at 3:25 PM Justin Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
>
>
>
>     On 4/2/20 3:19 PM, Surya Sanjay wrote:
>     > Hello all,
>     > I am a beginner Gromacs user and I have been using the Gromacs
>     tutorials on
>     > mdtutorials.com/gmx/ <http://mdtutorials.com/gmx/>. I would like
>     to simulate the binding of the
>     > infectious and normally-folded prion variants, and I want to
>     know if the
>     > protein-protein complex procedure is different from that of
>     protein-ligand
>     > systems.
>
>     A system containing several proteins is functionally no different
>     than
>     simulating one protein. Don't equate protein-protein systems to
>     protein-ligand systems, which often require external ligand
>     parametrization. None of that is necessary when dealing with proteins.
>
>     -Justin
>
>     -- 
>     ==================================================
>
>     Justin A. Lemkul, Ph.D.
>     Assistant Professor
>     Office: 301 Fralin Hall
>     Lab: 303 Engel Hall
>
>     Virginia Tech Department of Biochemistry
>     340 West Campus Dr.
>     Blacksburg, VA 24061
>
>     jalemkul at vt.edu <mailto:jalemkul at vt.edu> | (540) 231-3129
>     http://www.thelemkullab.com
>
>     ==================================================
>
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-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

==================================================