Unsolved

Hi guys,
I have some ligand structures in paper(overall structure). I want to convert those paper structure into pdb.(I have details about the bond order and bond distances).

So can someone can suggest me which is the best open source software to do this (I want to use generated ligand in liganddock application)

Thank in Advance
- K.Prasanth

Hi,

I searched for a basic protocol that can be used to minimize my four residue turn structure and I didn't find any. Therefore, I used the following method :-

scorefxn = create_score_function_ws_patch("standard","score12")
mm = MoveMap()
mm.set_bb(True)
pose_move_map.set_chi(True) ## For side chain minimization
mm.set_bb_true_range(1,4) ## Here range means 1 to 4 or the minimzation is applied only to residues 1 and4 ??

minmover = MinMover(mm, scorefxn, 'dfpmin', 10, True) ## I don't know the meaning of dfpmin,10,True. I saw it somewhere and used it

minmover.apply(pose)

I am working with calculating the rotamer-rotamer pairwise energies over the rotamer library for a fixed backbone. To do this I've essentially reimplemented the body of pack_rotamers_setup(), which ultimately calls RoatmersSet.calculate_energy(). I have a few questions on the topic, some of these are code-based others are to clear up my lack of biology background:

* What is the field RotamerSets.nmoltenres? This appears to be the number of rotamer positions, but is strictly less than the number of residues on the backbone. Shouldn't there be rotamers at every residue?

Hi all,

I am successfully using InterfaceAnalyzer to get a binding score between a protein and a peptide.
InterfaceAnalyzer is great in that it breaks down the score into different parameters.
However, I am looking to break down the score contribution into the contribution by each residue.

For instance, I'd like to know the hydrogen bond contribution of residue 6 (this is made up, but illustrates the point).
Or perhaps I'd like to know the vdw for residue 10. Etc.