[gmx-users] Parameterizing N-terminal capping

[Raji]

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?


Thanks

Raji




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>
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> Date: Tue, 27 Nov 2018 08:49:03 -0500
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Parameterizing N-terminal capping
> Message-ID: <afc683ab-3edd-df45-9772-546cef6fb940 at vt.edu>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
>
>
> 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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>
> ==================================================
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>