Re: Peptide planarity Dihedral angle restraints

From: Aron Broom (
Date: Thu Dec 08 2011 - 21:11:20 CST


I may be misunderstanding, but couldn't you just write a script that would
identify (or look through your coordinate file manually) the atom numbers
for the X-C-N-X atoms that make up the backbone, and then apply a harmonic
restraint for each? It would be a large restraint file no doubt, and
applying so many restraints might slow performance a bit.


On Thu, Dec 8, 2011 at 9:17 PM, Boyang Wang <> wrote:

> 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.
> Boyang
> 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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