Center of mass of a Protein

Question

[venu]

Hello,

I want to calculate center of mass of a protein. I know there are many tools servers out there to do this job but I've something more to do with it. I've gone through several sites to know about this. At last I've got to know something. Here they have shown something. What made me to come here are

1. While calculating do I need to consider every atom in the protein or just backbone is enough?
2. If I need to take all atoms how can I assign mass to every atom should I keep the mass constant? (because in this script they kept all atoms mass equal). Even if backbone is enough, should I assign the individual molecular mass to each amino acid in protein?
3. At last after solving the equation, how can I get the coordinates of the center of mass?

I just want to know what's going on beyond the equation which solves it.

Answer 1

[Woa]

For finding the CM taking uniform mass for each heavy atom (non hydrogen atom) is OK. Which equation you're talking about?

[venu]

This one..

http://pipe.ibibiosolutions.com/Com.html

[Woa]

The x,y,z co-ords of the Center of mass can be found out using the x,y,z co-ords of all the heavy atoms of the protein using that equation. That equation provides the CM as a position vector. Use this formula to individually calculate the X,Y,Z co-ord of the CM: http://formulas.tutorvista.com/physics/center-of-mass-formula.html