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 <jalem...@vt.edu
<mailto:jalem...@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
jalem...@vt.edu <mailto:jalem...@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
jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com
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