Re: Peptide planarity Dihedral angle restraints

From: Boyang Wang (
Date: Thu Dec 08 2011 - 20:17:02 CST

Hi Santhosh,

I agree. There are a limited number of impropers and you can try. It takes
a long time to find out all the impropers and you need the connections with
them. There is not a standard way of doing this.


On Fri, Dec 9, 2011 at 10:07 AM, Vijay Vammi <> wrote:

> 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

Boyang Wang, Ph.D.

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