[gmx-users] Regarding simulation radioactive material

[Justin Lemkul]

Again, please keep the discussion on the mailing list.

On 5/10/17 9:47 PM, RAHUL SURESH wrote:
> Dear Justin
>
> Thank you. I have to think over it a lot. To reparametarise a whole protein, I
> do not think it's possible or an easy job. The next pull down is the Change is
> mass should correspond to change in neutrons and should affect the stability of
> an atom which I don't whether it will work in any right way.
>
> Indeed, please let me know any possible way to reperameterize a molecule. I can
> simply try it with some single amino acids.
>

The way to parametrize anything is to follow the same protocol as the force 
field you're trying to modify.  In your case, the bonded terms would be 
essential because vibrational frequencies will change.  I doubt there will be 
differences in the nonbonded terms and doing anything like this strikes me as 
wasted effort because the MM approximation will likely view C-12 and C-14 as 
basically the same from the perspective of nonbonded interactions.

-Justin

>
> On Thu, 11 May 2017 at 1:35 A
> M, Justin Lemkul <jalemkul at vt.edu <mailto:jalemkul at vt.edu>> wrote:
>
>
>     Please keep the discussion on the gmx-users mailing list.  I am not a private
>     help service.
>
>     On 5/10/17 2:58 PM, RAHUL SURESH wrote:
>     > Dear Justin
>     >
>     > I would like to simulate a radioactive peptide.. I think this is the  first of
>     > its kind.  I wish to study interaction between Radioactive peptide and a
>     protein.
>     >
>     > To make it simple if I want to convert all my carbon into radioactive isotopes
>     > c14, and simulate is it possible ?
>     >
>
>     Possible, yes, but not correct.  If you change the mass of any atoms, you change
>     their vibrational frequencies, which means you need to reparametrize all the
>     bonded terms involving the modified atom types.  That means bonds, angles, and
>     dihedrals.  Whether or not this gives anything meaningful in terms of modeling
>     the interactions of a radioactive peptide with a larger protein is another
>     question.  If you're not changing any elements of the nonbonded terms (which you
>     likely shouldn't) then I doubt the interactions will be different in any
>     statistically meaningful way from the default parameters.  Re-doing bonded
>     parameters is a LOT of work.
>
>     -Justin
>
>     > References, I have found few  experimental papers on this. Where they have
>     Used
>     > isotopes of hydrogen. Tritium instead of hydrogen.
>     >
>     > If any information regarding this is available, will be a great use for me.
>     >
>     > Thank you.
>     > Sorry for writing in person
>     > --
>     > */Regards,/*
>     > */Rahul Suresh/*
>     > */Research Scholar/*
>     > */Bharathiar University/*
>     > */Coimbatore/*
>
>     --
>     ==================================================
>
>     Justin A. Lemkul, Ph.D.
>     Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
>     Department of Pharmaceutical Sciences
>     School of Pharmacy
>     Health Sciences Facility II, Room 629
>     University of Maryland, Baltimore
>     20 Penn St.
>     Baltimore, MD 21201
>
>     jalemkul at outerbanks.umaryland.edu <mailto:jalemkul at outerbanks.umaryland.edu>
>     | (410) 706-7441
>     http://mackerell.umaryland.edu/~jalemkul
>
>     ==================================================
>
> --
> */Regards,/*
> */Rahul Suresh/*
> */Research Scholar/*
> */Bharathiar University/*
> */Coimbatore/*

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================