[gmx-users] Parameterizing N-terminal capping

Justin Lemkul jalemkul at vt.edu
Tue Nov 27 14:49:17 CET 2018

On 11/26/18 1:50 PM, Raji wrote:
> Hi
> I am trying to parameterize the N-terminal ‘carboxybenzyl’ capping for
> peptide within CHARMM force field. Charges and bonded terms are transferred
> by analogy from available amino acid and lipid parameters. Grompp throwing
> errors for missing dihedral and bond terms of the linkage between ester
> group and peptide backbone. I appreciate any ideas.

You'll have to parametrize the missing interactions. Bonds and angles 
can probably be taken by analogy but should be verified. Dihedrals need 
to be parametrized by 1-D QM potential energy scans and then parameters 
fit to match.



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

Virginia Tech Department of Biochemistry
340 West Campus Dr.
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jalemkul at vt.edu | (540) 231-3129


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