Reply To: I am a beginner in rosetta software and need help to build params file

[Anonymous]

It doesn’t look like the enzdes/matcher constraint file documentation is all that well linked on the released manual, but http://www.rosettacommons.org/manuals/archive/rosetta3.2.1_user_guide/app_match_enzdes_cstfile.html is a direct link.

First off, it looks like you have the residue names and the atom names switched. Secondly, I don’t believe “residue4” is an allowed term. It should be either “residue1” (for one or more standard amino acids as one letter codes) or “residue3” (for natural and unnatural amino acid three letter code – “FE” counts as a three letter code – you may need a space after it to satisfy the parser, though). Keep in mind that “atom_name” takes three atom names the first is the one to which the distance is measured, the second helps define the angle, and the third helps define the torsion. Also, note that the atom name “N” refers to the backbone nitrogen of the amino acid – if you want the sidechain nitrogens, you’ll need to use “ND1” or “NE2” for the atom names of the delta or epsilon nitrogen, respectively. Or if you don’t care which one it is, you can specify “atom_type Nhis” for a deprotonated nitrogen or “atom_type Ntrp” for a protonated one (the matcher should consider multiple histidine protonation tautomers). “atom_type” will automatically figure out what the other two atoms should be based on the fold tree (the connectivity in the residue params file).

Finally, as you have a monoatomic atom for your “A” residue, you don’t really need to have extensive sampling of the angle_A, torsion_A or even the torsion_AB parameters. With the current settings, you’re going to spend a lot of time just spinning the virtual atoms all over the place. I’d recommend setting the periodicity of the A-side angles/torsions to 360 and the sampling parameter to 0 – this will minimize the time wasted placing the virtual atoms in different positions. Setting the distanceAB and B-side angles and torsions however you like should be sufficient to get the geometry to the histadine how you want it.