RosettaCommons - Chemically Modified Residues

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analyze_flex_ddG.py

valebut — Tue, 28 Nov 2023 12:30:07 +0000

Hello,

I am new to Rosetta. I am trying to perform the Flex ddG tutorial in order to predict changes in binding free energies upon mutation (interface ΔΔG).

I downloaded the folder from the GitHub webpage, and I succeesfully ran the run_example_1.py script which has generated three folders with one rosetta.out files (along with other files).

Then, I ran the python3 analyze_flex_ddG.py output/ command, and I get this error:

raceback (most recent call last):
File "/home/valeria/Downloads/flex_ddG_tutorial-master/analyze_flex_ddG.py", line 215, in <module>
analyze_output_folder( folder_to_analyze )
File "/home/valeria/Downloads/flex_ddG_tutorial-master/analyze_flex_ddG.py", line 191, in analyze_output_folder
ddg_scores, struct_scores = calc_ddg( scores )
^^^^^^^^^^^^^^^^^^
File "/home/valeria/Downloads/flex_ddG_tutorial-master/analyze_flex_ddG.py", line 132, in calc_ddg
ddg_scores = ddg_scores.append( scores.loc[ ((scores['state'] == 'unbound_wt') | (scores['state'] == 'bound_mut')) & (scores['struct_num'] <= nstructs) ].copy() )
^^^^^^^^^^^^^^^^^
File "/home/valeria/miniconda3/lib/python3.11/site-packages/pandas/core/generic.py", line 5989, in __getattr__
return object.__getattribute__(self, name)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'DataFrame' object has no attribute 'append'. Did you mean: '_append'?

Could you please help me understand what the problem is and how to solve it?

Thanks in advance

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Post Situation:

nomenclature question in molfile_to_params_polymer.py in ncaa design

lei — Tue, 21 Nov 2023 17:47:57 +0000

Dear users,

In NCAA tutorial, in order to use molfile_to_params_polymer.py script, we have to update the mol file by adding some additional data at the end of mol file.

Actually I understand most of these additional data except the meanings of POLY_UPPER and POLY_LOWER: they are atom number for capping groups connecting to the residue. However, I donot understand the UPPER and LOWER meanings in these two terms. They are connected to C-ter and N-ter of the residue, but is there any relationship between "UPPER & LOWER" and "C-ter & N-ter" of the residue?

Thanks!

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Post Situation:

RECCESS-Rosetta Segmentation Fault with nonnatural residues

skorro — Wed, 26 Jul 2023 00:13:26 +0000

Hello,

I am trying to run the recess-turner function with the following command:

recces_turner.macosclangrelease -score:weights stepwise/rna/turner -seq1 gu -seq2 [2MA]c -recces:n_cycle 9000000 -recces:temps 0.8 1 1.4 1.8 3 7 30 -st_weights 9.024828183205116 18.24157438187578 22.310063998885838 25.608533286161883 25.949659063278826 25.027484033009934 -recces:out_prefix ST -save_score_terms

I keep getting a segmentation fault when I use the 2MA modified residue. However, it is not all modified residues that fail. The following command works:

recces_turner.macosclangrelease -score:weights stepwise/rna/turner -seq1 gu -seq2 [3MC]c -recces:n_cycle 9000000 -recces:temps 0.8 1 1.4 1.8 3 7 30 -st_weights 9.024828183205116 18.24157438187578 22.310063998885838 25.608533286161883 25.949659063278826 25.027484033009934 -recces:out_prefix ST -save_score_terms

Please help why some modified residues work, and others don't.

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Post-traslational modifications

diegoms — Wed, 21 Jun 2023 08:22:59 +0000

Hello, everyone

I was trying to study the effect of post-translational modifications on the structure of proteins. For that purpose, I followed two different approaches:

I modified the residue with a variant using pyrosetta.rosetta.core.pose.add_variant_type_to_residue. Then, I replaced the original residue with the modified one using pose.replace_residue().
I tried using pyrosetta.rosetta.core.pose.add_variant_type_to_pose_residue to directly modify the residue in the pose.

In both cases, I obtained None as a result, but I would like to obtain a modified pose in order to calculate the ΔΔG value. Does anyone know how I can achieve that? Any suggestions would be appreciated.

Thanks in advance,

Diego

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PyRosetta - General

Post Situation:

Solved

N-Terminal Galactose

SebastianBB — Mon, 21 Nov 2022 16:33:59 +0000

Hi,

I want to modell the HbA1c (Hb with Galactose bound to the N-Terminal Val) N-Terminal residues.

I can't find a matching paramterset for the Galactose in the database. The to6-*-*-Galp.param is very close except that instead of the O6 atom, the C6 is bound to the N of the Val.

What is the best way to add the right parameters as a new residue type? Copy the to6-*-*-Galp.param files and modify just the atoms bound to the N or start from scratch?

How would the new *.param file look like?

Thanks a lot in advance,

Best regards,

Basti

Attachment	Size
GalVal.pdb	1.43 KB
GalVal.png	200.2 KB

Category:

Non-Canonical Peptides

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Rosetta 3 - General

Weekly releases for commercial users?

rjacak — Tue, 22 Mar 2022 14:48:27 +0000

Hi Steven, Rocco, et al.,

Would it be possible to have the weekly releases for commercial users restarted? The last weekly release available (for commercial users, maybe commercial and academic users?) is Rosetta 2021.16, with a release date of Friday, April 23, 2021. I know there have been bug fixes and other minor improvements made to apps that I am using and it would be great to have access to those. If weekly releases are unlikely to restart anytime soon, would it be possible to have the source code changes of bug fixes merged into main (master) posted somewhere so that licensees can patch the source themselves?

Thanks,
-Ron

Category:

Fragment Generation

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Rosetta 3 - General

Post Situation:

Modelling at defined pH - for pmutscan - pH:mode not working

cagfa1 — Tue, 15 Mar 2022 11:05:29 +0000

Hi all,

I am new to Rosetta and using various Rosetta protocols, primarily remodel and pmutscan, to assess the impact of various mutations on protein stability. I would like to model the protein and associated mutations at acidic pH as this may affect salt bridge formation and overall REU score.

I have tried using the -pH_mode true and -value_pH 2.5 flags as suggested in other posts (https://www.rosettacommons.org/node/3711). However, these flags do not have any effect on the protonation states of side chains in output pdb structures or on the calculated energy values.

Does anybody know how I could make these flags work? Do they still work on the most recent versions of Rosetta? Are there any other ways to take pH into account in Rosetta?

Thank you for any help!

My command looks like this:

pmut_scan_parallel.static.macosclangrelease -s 1tie_0008_0002_0004.pdb -database database -output_mutant_structures -DDG_cutoff 999 -ignore_unrecognized_res -no_his_his_pairE -multi_cool_annealer 10 -pH_mode -value_pH 2.5 -mute basic core -ex1 -ex2 > .sc

Category:

Scoring

Loop Modeling

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Post Situation:

RAbD with N-term，Proline-like ncaa returns segmentation fault during CCDEndsGraftMover

CordycepsLin — Mon, 07 Feb 2022 03:09:18 +0000

Recently I'm stumbling with rosetta RAbD application (version 2020.08.61146) in hope to modify an antibody whose antigen containing a non-canonical,N-term, and PRO-like aa ,namely the pyroglutamic acid in its epitope.

I generated params file according tutorials in :https://new.rosettacommons.org/demos/latest/public/design_with_ncaa/README,with input mol file below.

the product params runs properly during dock,relax,and RAbD's seq_design mode (except for wrong number in N-term hydrogen adding). but when doing graft design ,the application failed during CCDEndsGraftMover with a segmentation fault.

I had a series of attempts to solve the problem:

I fixed the patch file in database/chemical/residue_type_sets/fa_standard( and centroid ) /patches .

I tried to use Pro's centroid Params for this one. I tried to modify the ICOOR_INTERNAL lines so as to make the fold tree grows from CA (rather than from N , as the python script generated) ,adding virtual N and cut_bonds(as Pro's params does) .

I tried to change the value of NBR_RADIUS.

I even tried to modifying the params directly from PRO's by adding an acyl-oxgen atoms.

Below are two files I finally got. Sadly neither of them works. Due to limit error message, it's quite hard for me to debug the 'segmentation fault'.

Can anyone give it a look and help me out ?

thank you very much.

Attachment	Size
params_modified_from_PRO.txt	2.36 KB
params_gen_and_modified_manually.txt	1.99 KB
starting_pose_for_design.txt	145.47 KB

Category:

Design

Fragment Generation

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simple_cycpep_predict with N-term acetylation

Ken — Fri, 17 Dec 2021 17:49:41 +0000

Hi all,

I am trying to explore with simple_cycpep_predict using compstatin (from 2QKI as a toy example). This molecule is both N-term acetylated and C-term amidated, and I am having the hardest time trying to specify those modifications. As far as I understand it, simple_cycpep_predict doesn't use fasta format as input but uses space delimted 3 letter code to specify peptide sequence (the file that I am using is attached here). I tried using -extra_patch_fa with N_acetylated.txt but it doesn't seem to do anything. Can someone point me in the right direction?

Best,

Ken

Attachment	Size
compstatin.txt	51 bytes

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