Question: How To Calculate The Energy Function From The Coordinates Of Pdb File?
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gravatar for Priyanka
6.7 years ago by
Priyanka30
Priyanka30 wrote:

Dear Biostars!

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

Venerates

pdb bioinformatics • 2.6k views
ADD COMMENTlink modified 6.7 years ago by Pappu1.9k • written 6.7 years ago by Priyanka30
0
gravatar for Pappu
6.7 years ago by
Pappu1.9k
Pappu1.9k wrote:

try Discovery Studio.

ADD COMMENTlink written 6.7 years ago by Pappu1.9k

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

ADD REPLYlink modified 6.7 years ago • written 6.7 years ago by Priyanka30
1

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.

ADD REPLYlink modified 6.7 years ago • written 6.7 years ago by Pappu1.9k
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