From: Vijay Vammi (vsvammi_at_iastate.edu)
Date: Fri Dec 09 2011 - 00:47:00 CST
Right now I am trying to solve it by the tedious way of looking at atom
types. It might be easier for my case as the exact dihedral I am looking
for has the form X-C-N-X or X-C-NH1-X (or the reverse). With a good text
editor it was easy to change the required Kchis. But I also run into
simulation being unstable, this is expected to happen if the minimization
run was not enough. I am playing around with it.
I have thought of extra bonds feature but did not look much further as the
dihedral potential implemented is not sinusodial. This might cause the
simulation to become unstable if the angle changes from negative 179 to
-179, as far as I know. I might be wrong in my thinking.
The system would be subjected to accelerated Molecular Dynamics later and I
am not sure if the other features would go well with them. I would surely
check them if I dont have much luck in the tedius way. :-)
Thanks for your input,
On Fri, Dec 9, 2011 at 12:27 AM, Chris Harrison <charris5_at_gmail.com> wrote:
> 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
> char_at_ks.uiuc.edu Voice: 773-570-0329
> http://www.ks.uiuc.edu/~char Fax: 217-244-6078
> Vijay Vammi <vsvammi_at_iastate.edu> writes:
> > Date: Thu, 8 Dec 2011 20:07:12 -0600
> > From: Vijay Vammi <vsvammi_at_iastate.edu>
> > To: namd-l_at_ks.uiuc.edu
> > 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
> > 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
> > 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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