[gmx-users] Parameterizing N-terminal capping
jalemkul at vt.edu
Thu Nov 29 15:15:54 CET 2018
On 11/27/18 3:43 PM, Raji wrote:
> 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.
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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