[gmx-users] Parameterizing N-terminal capping

[Justin Lemkul]

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

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Justin A. Lemkul, Ph.D.
Assistant Professor
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Virginia Tech Department of Biochemistry
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jalemkul at vt.edu | (540) 231-3129
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