I used Rosetta Design to design a protein. I chose 10 independent trajectories, so I have now 10 different PDB files. Now I want to choose the sequence that produced the lowest energy, but I am not sure where I can find this information in the PDB files Rosetta Design produced. Does somebody know where I can see this information in these PDB files from Rosetta Design?
This is the information I can find in the PDB files:
- fa_atr: attractive portion of the Lennard Jones potential
- fa_rep: repulsive portion of the Lennard Jones potential
- fa_sol: Lazaridis-Karplus solvation energy
- fa_intra_rep: internal (within residue) Lennard Jones repulsive energy
- pro_close: proline closure energy
- fa_pair: pairwise electrostatics term derived from statistics on the pdb database
- hbond_sr_bb: hbond energy, short-range backbone-backbone
- hbond_lr_bb: hbond energy, long-range backbone-backbone
- hbond_bb_sc: hbond energy, backbone-sidechain
- hbond_sc: hbond energy, sidechain-sidechain
- dslf_ss_dst: disulfide energy terms
- dslf_cs_ang
- dslf_ss_dih
- dslf_ca_dih
- rama: ramachandran torsion energy derived from statistics on the PDB
- omega: omega angle energy
- fa_dun: rotamer energy derived from statistics on the PDB
- p_aa_pp: aa preference term; probability of seeing a given aa at given phi and psi angles
- ref: reference energy for this residue
- total: total energy for this resiude
I guess that "Total" should be about the energy information, but I wanted to be sure.
Thanks :)
I dont an specialist in this topic. But I recomend to use the http://raptorx.uchicago.edu/. For me is easy. Regards
Thanks, but that´s not the case. I mean, is not a problem with the software, the case is only that I don´t know exactly where to find the information I am looking for.
I am divided between "ref" and "total" .
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