RosettaCommons - Rosetta++ - General

READ ME FIRST

rmoretti — Fri, 04 Sep 2015 22:23:32 +0000

This is a forum dedicated to Rosetta++.

Development of Rosetta++ (aka Rosetta2) ceased around 2010.

The current version of Rosetta is Rosetta3 . -- Please see the Rosetta3 forums for help on using Rosetta3.

Access and support to Rosetta++ is provided primarily for recapitulation of previous results. It is highly recommended that all new projects use Rosetta3 rather than Rosetta++.

We will attempt to help you as much as possible with Rosetta++, but please be advised that Rosetta++ is no longer in frequent use.

Category:

Compilation

Forums:

Rosetta++ - General

Post Situation:

Solved

question about antibody modeling and snugdock process option

iojeong — Mon, 17 Apr 2023 02:18:13 +0000

I am currently working on a simple test with antibodies.

I have a question in this regard, can I use deepab instead of rosetta antibody to create antibody structures? When I looked at the snugdock paper, it seems that there is an additional protocol when using a tool other than rosetta antibody, but I know that deepab creates structures based on rosetta. So I am wondering if I can proceed in the same way as rosetta antibody when using deepab.

And I plan to superimpose the generated antibody and antigen to the original pdb to overlap, then prepack and snugdock.

Is there anything wrong with this process? I was wondering if the H3 modeling is a necessary part of it.

Also, one more question,

Since I need to run multiple tests, I'm also thinking of docking only the heavy chains considering the computing power, is it a problem to proceed this way?
In the paper on snugdock performance validation, it says that only heavy chains can be used, but I was wondering if this is only for nanobodies or if this is an option for antibodies as well.

And if it is, I would like to know how to use only heavy chains!

Category:

Docking

Forums:

Rosetta++ - General

Post Situation:

Unsolved

Building a PDB from a set of internal coordinates.

jcminerlanl — Mon, 06 Mar 2017 17:47:36 +0000

I am curious if anyone knows of a program in Rosetta that can build a protein or non-canonical polymer chain based on a set of internal coordinates and other geometric criteria?

Specifically I want to find a program that can take a set of dihedral angle data (with the possibility of including long-range, inter-residue contacts) and use these data to generate the Cartesian coordinates of the molecules.

If anyone knows of a particular program in Rosetta that can accomplish this, please point the way.

Category:

Structure prediction

Forums:

Rosetta++ - General

Post Situation:

Unsolved

error--rosetta fragment‐based refinement protocol for refinement against EM density

gsuchunli — Thu, 30 Jun 2016 18:06:53 +0000

I am trying to use rosetta fragment‐based refinement protocol for refinement against EM density. My script is attached.

It always complaints:

core.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.434133 seconds to load from binary
core.pack.pack_rotamers: built 185 rotamers at 21 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.interaction_graph.interaction_graph_factory: IG: 27768 bytes
protocols.rosetta_scripts.RosettaScriptsParser: dock_design_filename=A_asymm_refine.xml
protocols.rosetta_scripts.RosettaScriptsParser: Variable substitution will occur with the following values: '%%denswt%%'='25'; '%%map%%'='half1_34A.mrc'; '%%reso%%'='3.4'; '%%rms%%'='1.5'; '%%testmap%%'='half2_34A.mrc';
protocols.rosetta_scripts.RosettaScriptsParser: Substituted script:
<ROSETTASCRIPTS>
<SCOREFXNS>
<cen weights="score4_smooth_cart">
<Reweight scoretype=elec_dens_fast weight=20/>
</cen>
<dens_soft weights="soft_rep">
<Reweight scoretype=cart_bonded weight=0.5/>
<Reweight scoretype=pro_close weight=0.0/>
<Reweight scoretype=fa_sol weight=0.0/> # remove this line if not a membrane protein
<Reweight scoretype=elec_dens_fast weight="25"/>
</dens_soft>
<dens weights=“talaris2014_cart”>
<Reweight scoretype=elec_dens_fast weight="25"/>
<Reweight scoretype=fa_sol weight=0.0/> # remove this line if not a membrane protein
<Set scale_sc_dens_byres="R:0.76,K:0.76,E:0.76,D:0.76,M:0.76,C:0.81,Q:0.81,H:0.81,N:0.81,T:0.81,S:0.81,Y:0.88,W:0.88,A:0.88,F:0.88,P:0.88,I:0.88,L:0.88,V:0.88"/>
</dens>
</SCOREFXNS>
<MOVERS>
<SetupForDensityScoring name=setupdens/>
<LoadDensityMap name=loaddens mapfile=”half1_34A.mrc"/>
<SwitchResidueTypeSetMover name=tocen set=centroid/>
<MinMover name=cenmin scorefxn=cen type=lbfgs_armijo_nonmonotone max_iter=200 tolerance=0.00001 bb=1 chi=1 jump=ALL/>
<CartesianSampler name=cen5_50 automode_scorecut=-0.5 scorefxn=cen mcscorefxn=cen fascorefxn=dens_soft strategy="auto" fragbias="density" rms=1.5 ncycles=200 fullatom=0 bbmove=1 nminsteps=25 temp=4 fraglens=7 nfrags=25/>
<CartesianSampler name=cen5_60 automode_scorecut=-0.3 scorefxn=cen mcscorefxn=cen fascorefxn=dens_soft strategy="auto" fragbias="density" rms=1.5 ncycles=200 fullatom=0 bbmove=1 nminsteps=25 temp=4 fraglens=7 nfrags=25/>
<CartesianSampler name=cen5_70 automode_scorecut=-0.1 scorefxn=cen mcscorefxn=cen fascorefxn=dens_soft strategy="auto" fragbias="density" rms=1.5 ncycles=200 fullatom=0 bbmove=1 nminsteps=25 temp=4 fraglens=7 nfrags=25/>
<CartesianSampler name=cen5_80 automode_scorecut=0.0 scorefxn=cen mcscorefxn=cen fascorefxn=dens_soft strategy="auto" fragbias="density" rms=1.5 ncycles=200 fullatom=0 bbmove=1 nminsteps=25 temp=4 fraglens=7 nfrags=25/>
<ReportFSC name=report testmap=”half2_34A.mrc” res_low=10.0 res_high=3.4/>
<BfactorFitting name=fit_bs max_iter=50 wt_adp=0.0005 init=1 exact=1/>
<FastRelax name=relaxcart scorefxn=dens repeats=1 cartesian=1/>
</MOVERS>
<PROTOCOLS>
<Add mover_name=setupdens/>
<Add mover_name=loaddens/>
<Add mover_name=tocen/>
<Add mover_name=cenmin/>
<Add mover_name=relaxcart/>
<Add mover_name=cen5_50/>
<Add mover_name=relaxcart/>
<Add mover_name=cen5_60/>
<Add mover_name=relaxcart/>
<Add mover_name=cen5_70/>
<Add mover_name=relaxcart/>
<Add mover_name=cen5_80/>
<Add mover_name=relaxcart/>
<Add mover_name=relaxcart/>
<Add mover_name=fit_bs/>
<Add mover_name=report/>
</PROTOCOLS>
<OUTPUT scorefxn=dens/>
</ROSETTASCRIPTS>
Error: ERROR: Exception caught by JobDistributor while trying to get pose from job '3j5p_transmem_A_sym_0001'
Error: Tag::read - parse error, printing backtrace.

Tag::read - parse error - file:istream line:1 column:1 - <ROSETTASCRIPTS>
Tag::read - parse error - file:istream line:1 column:1 - ^

Error:

Error: Treating failure as bad input; canceling similar jobs
protocols.jd2.FileSystemJobDistributor: job failed, reporting bad input; other jobs of same input will be canceled: 3j5p_transmem_A_sym_0001
protocols.jd2.JobDistributor: no more batches to process...
protocols.jd2.JobDistributor: 1 jobs considered, 1 jobs attempted in 5 seconds
Error: ERROR: Exception caught by rosetta_scripts application:1 jobs failed; check output for error messages
Error:

My flags is the following:

-in:file:s 3j5p_transmem_A.pdb
-database /Applications/rosetta_2016/main/database
-out:suffix _sym
-ignore_unrecognized_res
-edensity:mapreso 3.4
-edensity:cryoem_scatterers
-parser:script_vars denswt=25 rms=1.5 reso=3.4 map=half1_34A.mrc testmap=half2_34A.mrc
-crystal_refine
-default_max_cycles 200
-overwrite
-parser:protocol A_asymm_refine.xml

Thanks,

Attachment	Size
A_asymm_refine.txt	2.74 KB

Category:

Design

Post Situation:

Unsolved

Forums:

Rosetta 3 - General

How to prepare the pdblist file for docking_ensmble in Rosetta3.4

sunlufinal — Tue, 02 Jun 2015 02:27:28 +0000

Did anyone do ensemble docking using rosetta3.4?
I don't know how to prepare those seemed like energy score(lowres_reference_energies_ , and highres_reference_energies_ from source code) at
the end of pdblist file?

An example of the pdblist is below:

input/xxip01_0001.pdb.ppk
input/xxip02_0001.pdb.ppk
input/xxip03_0001.pdb.ppk
input/xxip04_0001.pdb.ppk
input/xxip05_0001.pdb.ppk
input/xxip06_0001.pdb.ppk
input/xxip07_0001.pdb.ppk
input/xxip08_0001.pdb.ppk
input/xxip09_0001.pdb.ppk
input/xxip10_0001.pdb.ppk
3.91556
1.21555
3.651
5.58172
5.10037
0
5.55114
2.70723
1.01661
2.68865
-53.1856
-54.0107
-50.6703
-51.266
-55.8924
-55.34
-53.3811
-53.7216
-49.4558
-52.6443

Category:

Docking

Forums:

Rosetta 3 - General

Post Situation:

Unsolved

Consistency of interface DDG calculations

JuliusSu — Mon, 31 Mar 2014 04:35:02 +0000

Hello, I have been trying to validate interface energies computed using Rosetta 2.3, but have been having some difficulty obtaining agreement between two expressions that should be equivalent.

I start with a protein with two chains in a single PDB file, ab.pdb.

Then I run Rosetta++ with the following flags:
-interface -ddg_bind_only -s ab.pdb -intout ab.txt -output_structure -Wpack_only -relax_unbound false

This gives me three files:
ab_nat_0001.pdb (A chain only)
ab_nat_0002.pdb (B chain only)
ab_nat_0003.pdb (A+B chains together)

along with the following energies:
dG = E(AB) - E(A) - E(B) = (1253.7) - (672.7) - (639.4) = -58.4 final dG

Then I take each of the ab_nat_000*.pdb files, and rescore them using the following flags:
-s ab_nat_0001.pdb -score -fa_input -intout score.txt -overwrite -scorefile a.score

This time I obtain
E(AB) - E(A) - E(B) = (1253.7) - (669.5) - (634.4) = -50.3

which is different by 8 kcal/mol, because the energies of A and B are now different when scored separately.

The inconsistency persists despite trying many changes:
-- using softened potentials
-- relaxing structure beforehand
-- setting relax_unbound to false

Does anyone have any idea what could be causing these energy differences? Thanks!

Attachment	Size
ab.pdb_.txt	232.96 KB

Forums:

Rosetta++ - General

Post Situation:

Unsolved

How to allow rosetta to recognize the ASP and protonated ASP?

Jeffrey_Chen — Mon, 24 Mar 2014 07:41:13 +0000

Hi, everbody,
I'm using enzyme design to redesign a enzyme, and encountering a tough problem for me.
In the catalytic site, there is a protonated ASP, and a .cst file need to be given to constraint -OH of ASP and ligand.
Although I find the parameters of protonation state of ASP (ASP_P1.params or ASP_P2.params file) in the installation directory(.../rosetta_database/chemical/residue_type_sets/fa_standard/residue_types/protonation_states),
the 3 letter abbreviation of protonated ASP is also ASP, so I don't know how to inform the rosetta to recognize the ASPH.

I think a simple setting could sovle the problem, but it puzzuled me for a long time.Can someone give me a solution for this?

Thanks in advance for your suggestions.

Jeffrey Chen

Post Situation:

Unsolved

Forums:

Rosetta++ - General

weighted constraints

mintseris — Mon, 03 Feb 2014 23:24:57 +0000

I'm running abinitio with AtomPair constraints and would like to assign a weight to each constraint somehow based on its reliability. I've been looking at the many constraint functions under rosetta-3.5/rosetta_source/src/core/scoring/constraints/ many of which are not documented anywhere online that I can see and also at this post

https://www.rosettacommons.org/node/3344

I get the feeling that this should be somehow possible with existing code. If there was a way to multiply the result of each constraint score by some scalar sort of like ConstantFunc in the above post, maybe? The SkipViolFunc also seems like it's doing something similar, although I don't quite understand what. Before I dig deeper and start messing with the code, perhaps there's a relatively simple solution?

Thanks much

Post Situation:

Unsolved

Forums:

Rosetta++ - General

What's the difference between F and S labeled decoys?

PaulaBanks — Tue, 27 Aug 2013 06:44:18 +0000

Hi,

I am using rosetta 3.4 and in one case I got decoys labeled F_00000**** and in other cases they are labeled S_0000*****. What is the implication of this labeling?

Pauline.

Post Situation:

Unsolved

Forums:

Rosetta++ - General

About the code.What's the difference between .fwd.hh and .hh

Run — Sun, 21 Jul 2013 06:51:18 +0000

For example,CacheableData.fwd.hh and CacheableData.hh.What's the meaning of fwd?Help~~

Post Situation:

Unsolved

Forums:

Rosetta++ - General

RosettaCommons - Rosetta++ - General

READ ME FIRST

This is a forum dedicated to Rosetta++.

question about antibody modeling and snugdock process option

Building a PDB from a set of internal coordinates.

error--rosetta fragment‐based refinement protocol for refinement against EM density

How to prepare the pdblist file for docking_ensmble in Rosetta3.4

Consistency of interface DDG calculations

How to allow rosetta to recognize the ASP and protonated ASP?

weighted constraints

What's the difference between F and S labeled decoys?

About the code.What's the difference between ****.fwd.hh and ****.hh

About the code.What's the difference between .fwd.hh and .hh