You can do this in PyMOL:

https://pymolwiki.org/index.php/Center_of_mass

Hi Najme,

You can also use VMD software to calculate the center of mass.

Load .psf or .pdb in VMD and execute:

1) set sel [atomselect top "protein"]

2) mesure center $sel (to obtain geometric center)

3) measure center $sel weight mass (to obtain center of mass)

Hope it helps

Thanks

Gourav Shrivastav

Dear Gourav

Thank your replay.

using your command I take this for my protein:

>Main< (VMD) 4 % measure center $sel weight mass

-2.751770496368408 7.588507175445557 -0.08316531777381897

if I'm right, they are the x, y ,z coordinate of the center of mass. but I need to know which atom the center of mass hold on. how could I understand using VMD?

if you could help I'll really appreciated.

Dear Najme,

yes, these are x,y,z coordinates of your selection.

1) To select the atom and its corresponding residue or resname, select a small volume element in the vicinity of center of mass

set sel [atomselect top "x > -1 and x < 0 and y > 6 and y < 9 and z > -2 and z < 2"]

2) get the index of atom in this volume element

$sel get index

(you can tune the dimensions of the box defined in step #1 to get a single or few index)

3) get the residue id of the selected atoms

$sel get residue

4) get the residue name of the selected atoms

$sel get resname

Thanks

Gourav Shrivastav

Dear Gourav

your commands really worked and my problem was solved.

thank you very much.

dear Abdullahi Ibrahim Uba Rudy J Richardson, thank you for you replay.

Gourav Shrivastav

Hii Gourav,

I don't know can help. I am trying to calculate the center of mass of each monomer in a dimer. I tried using the method you described here but it did not work for each monomer , it only worked for the whole protein. I need the center of mass of each monomer because I want to calculate the distance between the two monomers that form the dimer. Gourav Shrivastav

You have to create a script which loops over every monomer and computes the distances:

For example

foreach i in (selection for monomer) {

set sel [atomselect top "fragment $i"]

set com1 [measure center $sel weight mass]

$sel delete

foreach j in (selection for monomer) {

set sel [atomselect top "fragment $i"]

set com2 [measure center $sel weight mass]

set dist [veclength [vecsub $com1 $com2]]

(you can write this distance to an output)

$sel delete

}

}

Gourav Shrivastav thanks