I have about 100000 PDB files and I need to calculate their free energy and total energy.
Does Rosetta3.4 have any such tool to calculate it ?
Depending on how you define "free energy" and "total energy", this is easy. Rosetta does not calculate in physical energy units (kcal/mol), it calculates in Rosetta Energy Units, which don't directly convert to physical energies. Read some of Kellog and Baker's papers on DDGs to learn how they've tried to get a scorefunction that reports in kcal/mol.
Anyway, if you'll take Rosetta's scores as answers, then make a file containing the filenames of all your pdbs (like, say "ls *pdb > pdblist"), and pass it to the score_jd2 app with the -l flag:
score_jd2.release -database /path/to/database -l pdblist -jd2:delete_old_poses
For 100,000, scoring is fast, but you may want to use MPI if it's available. (You need delete_old_poses to prevent a memory leak that occurs in this situation)
I am getting a scoring file (score.sc) which looks like
SCORE: score fa_atr fa_rep fa_sol fa_intra_rep pro_close fa_pair hbond_sr_bb hbond_lr_bb hbond_bb_sc hbond_sc dslf_ss_dst dslf_cs_ang dslf_ss_dih dslf_ca_dih rama omega fa_dun p_aa_pp ref linear_chainbreak overlap_chainbreak time description
SCORE: 2877.394 -266.363 3036.076 123.882 2.540 0.000 -2.674 -19.786 -16.727 -3.889 -1.492 0.000 0.000 0.000 0.000 -6.296 4.673 44.258 -9.408 -7.400 0.000 0.000 1.000 S_00000001_0001_0001
SCORE: 3615.740 -295.051 3789.284 142.326 2.541 0.000 -5.800 -19.779 -16.738 -4.709 -2.170 0.000 0.000 0.000 0.000 -6.300 4.668 44.277 -9.409 -7.400 0.000 0.000 0.000 S_00000001_0002_0001
SCORE: 464.803 -262.327 623.065 118.856 2.543 0.000 -2.091 -19.783 -16.736 -3.251 -1.320
Which part of this is generally used as the energy of the pdb molecule ?
The first column, marked "score", is the weighted sum of the other terms, and is used as the overall energy.
Those are scores that indicate Rosetta hates the structures, BTW - you should have something like -2 per residue, you have something positive. The positivity is in your fullatom repulsive (fa_rep) term.
It is a dimer so may be that is why it is positive.
No...if there are 100 residues total, you should expect fullatom scores between -100 to -300, depending on the quality of the structure. A positive score means Rosetta things the structure has a positive folding energy - in other words it won't fold that way. (Usually this is due to a clash).
Keep in mind that "clashes" are *very* common in structures which come directly from the PDB. Rosetta's energy function is sensitive enough that small coordinate changes which aren't necessarily experimentally relevant can have a great effect on the reported energy. (And even a small clash in some distal part of the protein can greatly affect the score.)
It's commonly suggested that from-PDB structures should be relaxed into the Rosetta energy function before relying on the score. The recently-released Rosetta 3.4 now has a simple protocol to do a heavy-atom constrained relax, which in our experience can greatly improve the energy without significantly changing the atom positions (i.e. all-atom RMSDs in the tenths of angstoms). ( See http://www.rosettacommons.org/manuals/archive/rosetta3.4_user_guide/d9/d..., sections labeled with "Relax with all-heavy-atom constraints")