RosettaCommons - Rosetta++ - Applications

READ ME FIRST

rmoretti — Fri, 04 Sep 2015 22:26:09 +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++ - Applications

Post Situation:

Solved

Error when running the CstfileToTheozymePDB Application

jkoch19 — Mon, 18 Dec 2023 16:34:32 +0000

Hello,

I am relatively new to Rosetta, and i am trying to generate a constraint file (.cst) with my catalytic amino acid and ligand defined, that i am going to use to search against a PDB database. However, no matter how hard i try i keep obtaining this error:

protocols.toolbox.match_enzdes_util.InvrotTree: A total of 112 unique definitions of the invrot tree exist.
protocols.toolbox.match_enzdes_util.InvrotTree: Writing definition 1 to file PDB_Model_RD-2.cst_1.pdb...
protocols.toolbox.match_enzdes_util.InvrotTree: 100 invrots for list 0, 54 invrots for list 1, 15 invrots for list 2, 10 invrots for list 3, 234 invrots for list 4, 10 invrots for list 5,

ERROR: Assertion `serial_to_serial_with_ter.count(ai.connected_indices[ c_index ] )` failed.
ERROR:: Exit from: src/core/io/pdb/pdb_writer.cc line: 616

[ ERROR ]: Caught exception:

File: src/core/io/pdb/pdb_writer.cc:616
[ ERROR ] UtilityExitException
ERROR: Assertion `serial_to_serial_with_ter.count(ai.connected_indices[ c_index ] )` failed.

I appreciate all help i can get at this point! Thank you

Attachment	Size
Params file of my ligand	7.83 KB
CST File	3.38 KB
Rosetta Crash log	1.31 KB

Category:

Enzyme Design

Post Situation:

Unsolved

Forums:

Rosetta++ - Applications

How to use 'CYZ' residues?

Seongsung — Fri, 03 Jun 2022 08:40:50 +0000

Hi, all.

I want to refine a PDB file with one zinc ion using 'SetupMetalsMover'.

I have added one zinc ion which is predicted to coordinate with cysteine and histidine.

I noticed there is 'CYZ.params' file and 'residue_types.txt' file ( '/database/chemical/residue_type_sets/fa_standard/residue_types.txt' file ) includes the 'CYZ.params'.

Then, I changed the residue name of cysteine to 'CYZ' (from CYS).

And then, I executed rosettascript to refine my pdb.

But, error has occured and showed as below.

------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

core.chemical.GlobalResidueTypeSet: (0) {0} Loading (but possibly not actually using) 'CYZ' from the PDB components dictionary for residue type 'pdb_CYZ'
core.io.pose_from_sfr.PoseFromSFRBuilder: (0) {0} Adding undetected upper terminus type to residue 44, 44 A
core.io.pose_from_sfr.PoseFromSFRBuilder: (0) {0} Adding undetected upper terminus type to residue 99, 99 A
core.io.pose_from_sfr.PoseFromSFRBuilder: (0) {0} [ WARNING ] discarding 6 atoms at position 45 in file TaCA_zinc_input.pdb. Best match rsd_type: pdb_CYZ
core.io.pose_from_sfr.PoseFromSFRBuilder: (0) {0} [ WARNING ] discarding 6 atoms at position 100 in file TaCA_zinc_input.pdb. Best match rsd_type: pdb_CYZ
core.conformation.Conformation: (0) {0} [ WARNING ] missing heavyatom: OXT on residue THR:CtermProteinFull 44
core.conformation.Conformation: (0) {0} [ WARNING ] missing heavyatom: C1 on residue pdb_CYZ 45
core.conformation.Conformation: (0) {0} [ WARNING ] missing heavyatom: C2 on residue pdb_CYZ 45
core.conformation.Conformation: (0) {0} [ WARNING ] missing heavyatom: C3 on residue pdb_CYZ 45
core.conformation.Conformation: (0) {0} [ WARNING ] missing heavyatom: C4 on residue pdb_CYZ 45
core.conformation.Conformation: (0) {0} [ WARNING ] missing heavyatom: C5 on residue pdb_CYZ 45
core.conformation.Conformation: (0) {0} [ WARNING ] missing heavyatom: C6 on residue pdb_CYZ 45
core.conformation.Conformation: (0) {0} [ WARNING ] missing heavyatom: C7 on residue pdb_CYZ 45
core.conformation.Conformation: (0) {0} [ WARNING ] missing heavyatom: C8 on residue pdb_CYZ 45
core.conformation.Conformation: (0) {0} [ WARNING ] missing heavyatom: N1 on residue pdb_CYZ 45
core.conformation.Conformation: (0) {0} [ WARNING ] missing heavyatom: S1 on residue pdb_CYZ 45
core.conformation.Conformation: (0) {0} [ WARNING ] missing heavyatom: C9 on residue pdb_CYZ 45
core.conformation.Conformation: (0) {0} [ WARNING ] missing heavyatom: C10 on residue pdb_CYZ 45
core.conformation.Conformation: (0) {0} [ WARNING ] missing heavyatom: N2 on residue pdb_CYZ 45
core.conformation.Conformation: (0) {0} [ WARNING ] missing heavyatom: C11 on residue pdb_CYZ 45
core.conformation.Conformation: (0) {0} [ WARNING ] missing heavyatom: C12 on residue pdb_CYZ 45
core.conformation.Conformation: (0) {0} [ WARNING ] missing heavyatom: C13 on residue pdb_CYZ 45
core.conformation.Conformation: (0) {0} [ WARNING ] missing heavyatom: C14 on residue pdb_CYZ 45
core.conformation.Conformation: (0) {0} [ WARNING ] missing heavyatom: CL on residue pdb_CYZ 45
core.conformation.Conformation: (0) {0} [ WARNING ] missing heavyatom: S2 on residue pdb_CYZ 45
core.conformation.Conformation: (0) {0} [ WARNING ] missing heavyatom: O1 on residue pdb_CYZ 45
core.conformation.Conformation: (0) {0} [ WARNING ] missing heavyatom: O2 on residue pdb_CYZ 45
core.conformation.Conformation: (0) {0} [ WARNING ] missing heavyatom: O3 on residue pdb_CYZ 45
core.conformation.Conformation: (0) {0} [ WARNING ] missing heavyatom: O4 on residue pdb_CYZ 45
core.conformation.Conformation: (0) {0} [ WARNING ] missing heavyatom: N3 on residue pdb_CYZ 45

ERROR: too many tries in fill_missing_atoms!
ERROR:: Exit from: src/core/conformation/Conformation.cc line: 1855
Error: (0) {0} [ ERROR ] ERROR: Exception caught by JobDistributor while trying to get pose from job 'input_0001'
Error: (0) {0} [ ERROR ] Treating failure as bad input; canceling similar jobs

[ ERROR ]: Caught exception:

File: src/core/conformation/Conformation.cc:1855
[ ERROR ] UtilityExitException
ERROR: too many tries in fill_missing_atoms!

I guess I might have lost something, but I don't know what it is...

I'm using 'Rosetta 2021.38'.

Any suggestion would be greatly appreciated.

Thanks all.

Category:

Enzyme Design

Forums:

Rosetta++ - Applications

Post Situation:

Unsolved

Distinctions between InterfaceAnalyzer and RosettaScript

achambe — Wed, 17 Jun 2015 17:14:48 +0000

Hi,

I am currently working to develop a protocol to compute the destabilization of the interface between two proteins upon mutation. The characteristics that I am looking for are a methodology that will distinguish between the perturbation induced by a mutation at the surface and one that is buried, and a perturbation that leads to destabilization of the interface versus one that does not. Thus my general strategy is to compute the energy of binding for the wild type and for the mutant and then take the difference. Because the initial structures are taken from crystal structures, I allow for repacking of the sidechains for both wildtype and mutant before computing the binding energy. From perusing the forums and sundry papers recommended there I either modified or created three different protocols. As far as I understand, the primary distinction lies in either scoring or the packing used however I am not clear how so. From my perspective they should in principle produce the same trends though perhaps not the same numbers, they do not and I am left a bit perplexed. I found that protocol 3 produces the qualitative behaviors I expected however I am somewhat unsure at this point how it differs from protocols 1 and 2. I know that in one fashion or another this question has been hashed and rehashed however having spent alot of time trying to figure out why these different methods produce wildly different results, I figured it might be nice to clarify this in a single spot. Your thoughts and insight regarding how the protocols differ would be very welcome.

Protocol 1:
Commandline:
InterfaceAnalyzer.default.linuxgccrelease @options -s <FILENAME>

options file:
-overwrite
-interface A_B
-pack_input true
-pack_separated true
-out:file:score_only score.sc

The initial sidechains are built externally and a prebuilt PDB was fed in. This was done because as I understood it the InterfaceAnalyzer when called alone did not handle resfiles. As I understand, it uses the default score12 weights. While the mutation is done in an external program I thought that since the sidechain is repacked, this would not introduce a significant issue.

Protocol 2:
Commandline:
rosetta_scripts.linuxgccrelease @options -s <FILENAME>

options file:
-parser:protocol interface_analysis.xml
-score12prime true
-ignore_unrecognized_res
-no_his_his_pairE
-out:file:score_only score.sc
-no_optH false
-ex1
-ex2
-use_input_sc
-extrachi_cutoff 1
-linmem_ig 10
-ignore_unrecognized_res
-atomic_burial_cutoff 0.01
-sasa_calculator_probe_radius 1.2
-overwrite

interface_analysis.xml:
<ROSETTASCRIPTS>
<SCOREFXNS>
<s12_prime weights="score12prime"/>
</SCOREFXNS>
<TASKOPERATIONS>
</TASKOPERATIONS>
<MOVERS>
<InterfaceAnalyzerMover name=fullanalyze scorefxn=s12_prime packstat=1 pack_input=1 pack_separated=1 jump=1 tracer=0 use_jobname=1 resfile=0/>
</MOVERS>
<PROTOCOLS>
<Add mover_name=fullanalyze/>
</PROTOCOLS>
</ROSETTASCRIPTS>

As I understand this protocol primarily differs from the 1st in terms of possibly allowing for extra chi angles in the rotamer sampling.

Protocol 3:
Commandline:
rosetta_scripts.linuxgccrelease @resfile.flags

resfile.flags file:
-parser:protocol mutation_script.xml
-s 2O8B.pdb
-ignore_unrecognized_res
-out:file:score_only score.sc
-nstruct 1
-overwrite

mutation_script.xml:
<dock_design>
<SCOREFXNS>
</SCOREFXNS>
<FILTERS>
Here we add two delta G filters to calculate the delta G of binding before and after mutations are made.
We specify a jump number of 3 because want to calculate the delta G of binding the ligand, which is chain D
in the given PDB file.
<Ddg name=dg_wt threshold=1000 repeats=50 jump=1/>
<Ddg name=dg_mut threshold=1000 repeats=50 jump=1/>
</FILTERS>
<TASKOPERATIONS>
Here we add a task operation used to specify that we want only to repack residues without design
<RestrictToRepacking name=repack_only />
Here we specify the location of the resfile to use for design.
<ReadResfile name=resfile filename=mut.resfile/>
</TASKOPERATIONS>
<MOVERS>
Here is a mover to relax the crystal structure
FastRelax name=relax/>
Here we pack the rotamers without any design
<PackRotamersMover name=pack scorefxn=talaris2013 task_operations=repack_only/>
Here we pack the rotamers with design. We specify to read the resfile containing the mutation we want to design
<PackRotamersMover name=mut_and_pack scorefxn=talaris2013 task_operations=resfile/>
</MOVERS>
<PROTOCOLS>
Here we include the movers and filters in the order we want them to run
Add mover_name=relax/>
<Add mover_name=pack/>
<Add filter_name=dg_wt/>
<Add mover_name=mut_and_pack/>
<Add filter_name=dg_mut/>
</PROTOCOLS>
</dock_design>

mut.resfile:
NATAA
EX 1 EX 2
USE_INPUT_SC
AUTO
start
<RESIDUE NUMBER> A PIKAA <RESIDUE CHANGE>

The last protocol differ from the first two in the fact that mutations are handled using a resfile rather than reading in a pre-mutated pdb, it also allows for the specification of several more repeats of the initial sampling (50 repeats in this case), rather than requiring repeated runs from the external commandline (not shown) to obtain statistical sampling. However other than these distinctions I am not clear how exactly it differs from the preceding protocol. As I said before thoughts and suggestions would be most welcome. Thank you for your consideration in advance.

Category:

Scoring

Forums:

Rosetta 3 - Applications

Post Situation:

Unsolved

latest version of rosetta unable to build models

pramod — Mon, 03 Nov 2014 19:31:47 +0000

hi,

I have been successfully following the protocol as per the paper "Small-molecule ligand docking into comparative models with Rosetta" to build the homology models of transporters using Rosetta 3.5. However, recently, after installing the latest version of rosetta :rosetta_2014.35.57232_bundle and tried to build the models using the protocol as mentioned in the paper (mentioned above) I could not build the models. The program is running without errors but could not fold the protein. I was wondering if i have to follow a different protocol for the latest version of rosetta? and how this issue could be fixed?

Please let me know your suggestions.

Thanks,
Pramod

Category:

Structure prediction

Forums:

Rosetta 3 - Applications

Post Situation:

Unsolved

ab initio modeling using constraints

shrutikhare — Fri, 07 Feb 2014 09:03:52 +0000

I am working on ab initio folding of a dimeric molecule using distance constraints.
The constraints format being used is similar to NMR derived NOE constraints.
But, data is not derived from NMR.
I was wondering if that is the correct way to impose constraints on any general
system.

Flagfile:
~/rosetta. -seed_offset `echo $RANDOM` -cst ~/test.cst -cst_min -nstruct 10000
-paths ~/paths.txt -output_pdb_gz -timer -fa_output -output_silent_gz
-read_all_chains -randomize1 -symm_type cn -pose_fold_and_dock
-docking_pose_symmetry -pose1 -slide_contact_frequency 0.01
-rigid_body_frequency 0.01 -rigid_body_cycles 100 -new_centroid_packing
-rg_reweight 0.0001 -move_anchor_points -monomer_input -pose_relax
-pose_relax_fragment_moves -increase_cycles 1 -output_chi_silent
-stringent_relax -ex1 -ex2 -vary_omega -omega_weight 0.5
-docking_pose_symm_full -combinatorial_rms_sym
-pose_symm_jump_moves_during_relax -pose_symm_n_monomers 2

constraint format I am using:
5 CEN 16 CEN 7.00 4.00
5 CEN 81 CEN 7.00 4.00
5 CEN 36 CEN 7.00 4.00
36 CEN 63 CEN 7.00 4.00

I am using rosetta v2.3.
Are all these flags in order?
Is there any other way of performing constraint based ab initio folding?

Thanks in advance.

Post Situation:

Unsolved

Forums:

Rosetta++ - Applications

Epi-Graft Match

cruc12 — Thu, 24 Oct 2013 18:56:53 +0000

Hi,
I see the following errors when running epi-graft. What commands do I need to overcome these limits?
Thank you very much in advance for your help!

STOP :: MAX_PACK_NEIGHBORS exceeded
MAX_PACK_NEIGHBORS: 100
ERROR:: Exit from: pack.cc line: 5280

STOP:: MAX_HB_PER_ATM exceeded
ERROR:: Exit from: hbonds.cc line: 665

STOP:: acc MAX_HB_ATM exceeded
ERROR:: Exit from: hbonds.cc line: 623

STOP:: don MAX_HB_ATM exceeded
ERROR:: Exit from: hbonds.cc line: 635

*****ERROR TOO MANY CYSTEINES COUNTED*****
ERROR:: Exit from: disulfides.cc line: 644

Post Situation:

Unsolved

Forums:

Rosetta++ - Applications

missing ram_buildloop_wrapper4.pl in rosetta antibody modeller

jchin — Mon, 12 Nov 2012 03:31:53 +0000

Rosetta 2.3.0
Python 2.4.3
Run on cluster

I'm attempting to setup rosetta antibody but encounter the error message below( script ram_buildloop_wrapper4.pl is missing).
My installation is rosetta 2.3.0. The script doesn't seem to be in rosetta++ or rosetta3 either.
[…@login-0-0 test]$ perl -P ../antibody/scripts/ram_buildloop_wrapper4.pl ../antibody/database/pdb1xyz_chothia.pdb bit ram ram 1 1 1 1 1 0 0 1 1 0 0 0 0 FR 02 2 1 3 2000 2000 3 0 ../1dqq_h.fasta 1dqq_l.fasta

/home/…/immunity/test

Can't open /home/…/immunity/antibody/scripts/ram_create_query_fasta.pl: No such file or directory.

These are the contents of the script directory:

[…@login-0-0 scripts]$ ls

build ram_assignnumbering.pl ram_create_query_database.pl ram_print_residues_fromfasta.pl

fasta.blast ram_blankcdrs.pl ram_create_rmsd_table_h3frags.pl ram_profit_script_h3frags.pl

get_cterm_residues.pl ram_blastscript_h3frag.pl ram_id_perfect_matches.pl ram_profit_script.pl

get_mer_from_fasta.pl ram_blastscript.pl ram_kink_query.pl ram_read_matches.pl

getminimum_per_identity.pl #ram_buildloop_wrapper4.pl# ram_make_rosetta_fragments.pl ram_setup_rrun2.pl

make_rosetta_fragments.pl ram_buildloop_wrapper4.pl ram_mapping1.pl readdsspline.pl

paths.txt ram_cluster_h3frags.pl ram_match_hacks.pl read_h3pseudodihedral.pl

pdb_cleaner.pl ram_copytemplates1.pl ram_members_of_list.pl readinfo.pl

ram_analyze_blast8.pl ram_create_condor_script.pl ram_mutate_pdb2.pl readpdbline.pl

ram_analyze_blast_h3frag.pl ram_create_H3CterNter2.pl #rampaths.txt# removespaces.pl

ram_append_abfrags_to_rosettafrags2.pl ram_create_query_database_lightheavy.pl rampaths.txt utilities.txt

Thanks!

Post Situation:

Unsolved

Forums:

Rosetta++ - Applications

Problems with the convergence of docking by the graph

Kanorgon — Sun, 25 Mar 2012 11:56:59 +0000

I have been doing the docking with the program Rosetta
for an antigen-antibody complex
repeated runs and not get a graph
funnel-shaped
because the lowest energy structure
have a higher rmsd 5Ǻ
wanted to know if that's possible
really appreciate the attention you can give me.

PS
attached a file with the results in pdf format

In these cases it will be worth re-do the docking from some of the results, ie, do a re-docking of the structure obtained in order to obtain a better convergence?

Attachment	Size
docking Job.pdf	326.43 KB

Forums:

Rosetta++ - Applications

Post Situation:

Unsolved

refinement or idealization of a dimeric protein

anusmita — Thu, 24 Feb 2011 06:23:53 +0000

Hii All

I am looking forward for idealizing and then refining a dimeric protein , but, using a fragment library for a monomeric protein. Use of a dimeric fragment library joins the two monomers into one single protein chain.

Thanking you

Post Situation:

Unsolved

Forums:

Rosetta++ - Applications