[gmx-users] Parameterizing N-terminal capping

Justin Lemkul jalemkul at vt.edu
Thu Nov 29 15:15:54 CET 2018

On 11/27/18 3:43 PM, Raji wrote:
> Hi
> Thank you for your reply. To parameterize the dihedrals, OSL-CL-NH1-H,
> OSL-CL-NH1-CT1, NH1-CL-OSL-CTL2 (OSL,CL, CTL2 from carboxy benzyl capping
> and NH1, H, CT1 from peptide backbone) How to segment the molecule with
> peptide backbone?

The model compound for parametrization needs to be large enough to 
encompass all the degrees of freedom that need to be parametrized, with 
suitable capping groups to mimic any neighboring chemical moieties.



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


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