Re: Peptide planarity Dihedral angle restraints

From: Vijay Vammi (vsvammi_at_iastate.edu)
Date: Thu Dec 08 2011 - 21:20:23 CST

@Boyang : Thanks for the information. I am thinking of a script to do the
same thing I do manually.

@Aron: I dont want to add restraints externally to the system, increasing
the force constant Kchi would best serve my purpose. It worked very well in
AMBER FF. But thanks for the suggestion.

On Thu, Dec 8, 2011 at 9:11 PM, Aron Broom <broomsday_at_gmail.com> wrote:

> Santosh,
>
> 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.
>
> ~Aron
>
>
> On Thu, Dec 8, 2011 at 9:17 PM, Boyang Wang <pkuwangboyang_at_gmail.com>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 <vsvammi_at_iastate.edu> 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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