prepare PDB with constrained relax

[Anonymous]

Hi,

When I were preparing some PDB files of crystal structures for Rosetta simulation, there are several ways to go after I checked Rosetta manuals and demos.

First method is following the doc ‘Documentation for relax pdb with all-atom constraints / prepare pdb for rosetta with relax’ in user guide and the codes in demos/prepare_pdb_for_rosetta_with_relax/. Breifly, it is using “relax” with some extra options e.g. ‘-relax:constrain_relax_to_start_coords’.

Another method is mentioned in doc ‘Documentation for ddg_monomer application’ where a helper application ‘minimize_with_cst’ is used.

I have no idea what is the difference between the two approaches and which one is more preferable in practical applications. So anyone can give some details about the backends?

Personally I prefer ‘minimize_with_cst’ because it can keep the original chain IDs in PDB, while ‘relax’ always renumbers the chain IDs to ‘A B C D …’ even the option “-out:file:renumber_pdb false” is used.
Is there any way to let ‘relax’ not to renumber chain IDs?

cheers,

[Anonymous]

Unfortunately, coordinate constrained relax will always renumber PDBs – at least with Rosetta3.4 and before.

The problem is that in order to properly constrain the coordinates of the residues, relax adds and then removes a “virtual root” atom. The process of adding and deleting a residue results caused Rosetta to renumber the entire PDB.

This has been fixed for upcoming Rosetta3.5 release, so coordinate constrained relax will no longer renumber the PDB.

**

Regarding the difference between constrained relax and minimize, constrained relax is a bit more aggressive in its optimization. It does cycles of packing and minimization with ramping repulsive, so it can better rework hydrogen bonding networks and do a more effective local search. It also consequently takes longer. If speed is not an issue, I’d recommend the constrained relax (though I have access to the version which doesn’t renumber PDBs).

[Anonymous]

Thank you for the comments.
I am looking forward to version 3.5.
Indeed, constrained relax takes much longer than minimize, and somehow my MPI-compiled version does not boost the calculation. If the MPI works, the speed is more comfortable .

[Anonymous]

Most protocols in Rosetta are parallelized at the output structure level – each output structure can be run in parallel, but a single output structure doesn’t gain anything from being run with MPI. There are some protocols that benefit greatly from MPI even for a single output, but relax is one where MPI gains will only be realized when doing multiple output structures.

[Author]

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