Question: Center of mass of a Protein
0
gravatar for venu
4.0 years ago by
venu6.0k
Germany
venu6.0k wrote:

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 (http://pipe.ibibiosolutions.com/Com.html) 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? (be cause in this script they kept all atoms mass equal https://code.google.com/p/pdb-tools/source/browse/trunk/pdbTools/pdb_centermass.py). 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 whats going on beyond the equation which solves it.

ADD COMMENTlink modified 4.0 years ago by Woa2.7k • written 4.0 years ago by venu6.0k
0
gravatar for Woa
4.0 years ago by
Woa2.7k
United States
Woa2.7k wrote:

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

ADD COMMENTlink written 4.0 years ago by Woa2.7k

This one..

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

ADD REPLYlink written 4.0 years ago by venu6.0k

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 invidually calculate the X,Y,Z co-ord of the CM:
http://formulas.tutorvista.com/physics/center-of-mass-formula.html

 

ADD REPLYlink written 4.0 years ago by Woa2.7k
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