How To Calculate The Energy Function From The Coordinates Of Pdb File?

Question

[Priyanka]

Dear Biostars!

Could anyone tell me how to calculate energy from the coordinates of PDB file using a standalone program?

Venerates

Answer 1

[Pappu]

try Discovery Studio.

[Priyanka]

Ya, but only the licensed version has the option of calculating the energy

[Pappu]

A friend of mine was asking me the same question recently. In any molecular dynamics (MD) program like Gromacs, CHARMM or AMBER, there are energy minimization procedures in different forcefields. There you can find out the initial energy and change during minimization. SInce the pdb file is already minimized, the change in energy during minimization will be low. Having said that, all MD programs have steep learning curve. Try charmm-gui (google it) for web interface to charmm. You can see also gromacs tutorials.

Alternatively vmd has a plugin: www.ks.uiuc.edu/Development/MDTools/mdenergy/ or http://code.google.com/p/pdb-tools/ can calculate energy of a pdb file.

It all depends on your research objectives.