Re: Peptide planarity Dihedral angle restraints

From: Chris Harrison (
Date: Fri Dec 09 2011 - 00:27:29 CST


You could do this by:

1) preparing your own CHARMM parameter file with all the specific
atom-types of the dihedrals needed (granted a tedious undertaking)

2) extrabonds

3) colvars with a) ABF, b) metadynamics, or c) harmonic restraints

4) tclforces


Chris Harrison, Ph.D.
Theoretical and Computational Biophysics Group
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801                          Voice: 773-570-0329              Fax:   217-244-6078
Vijay Vammi <> writes:
> Date: Thu, 8 Dec 2011 20:07:12 -0600
> From: Vijay Vammi <>
> To:
> Subject: namd-l: Peptide planarity Dihedral angle restraints
> Hello all,
> During MD simulation, I want to put additional restraints to maintain
> peptide planarity.
> In AMBER forcefields, i was able to do it by increasing the Kchi value for
> X-C-N-X. (in the parm99.dat).
> In CHARMM forcefields, as far as I know, wildcards would be accepted only
> if there is no specific combination found. One way of solving this would be
> to
> 1). For every peptide bond, find all the atomtypes combination(eg:
> CA-C-N-CA could be CT1-C-N-CT1 and many other possibilities) and increase
> the Kchi value in the parameter file.
> Is there any other simple way?
> Thanks
> Santhosh

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