RosettaCommons - Constraints

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PyRosetta - General

Post Situation:

Failure to produce a cst file

biotech — Wed, 26 Oct 2022 18:17:14 +0000

Hi, I generated a mincst.log using the below command:

minimize_with_cst.default.linuxgccrelease -s fe.pdb -in:file:fullatom -ignore_unrecognized_res -fa_max_dis 9.0 -database /home/protein-institute/ROSETTA/rosetta_bin_linux_2020.08.61146_bundle/main/database -ddg::harmonic_ca_tether 0.5 -ddg::constraint_weight 1.0 -ddg::out_pdb_prefix min_cst_0.5 -ddg::sc_min_only false > mincst.log

then produced mincst.log file was employed for generating a cst file as input for the high-resolution protocol of ddg_monomer using the below command:

convert_to_cst_file.sh mincst.log > i.cst

unfortunately, the process was disrupted and cst file haven't the necessary information. all input and output files were uploaded.

Attachment	Size
mincst.txt	124.16 KB
convert_to_cst_file.txt	612 bytes

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Post Situation:

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Residue outside res_map range

to-qinbin@163.com — Sat, 10 Sep 2022 08:56:46 +0000

Hi, I am using Rosetta to relax a enzyme with a substrate and a cofactor. The "flags2" was from rosetta/main/demos/public/prepare_pdb_for_rosetta_with_relax/starting_inputs

The params file for substrate (DHD.params) and cofactor (NAP) were also used.

But errors!! How to solve this problem?

"flag2" was scucessfull for the "1A99_1A99.pdb" inrosetta/main/demos/public/prepare_pdb_for_rosetta_with_relax/starting_inputs

(base) ubun@ubun-System-Product-Name:~/relax/test$ $ROSETTA/main/source/bin/relax.mpi.linuxgccrelease -s 01-MD-086DS.pdb @flags2 > log2.txt

[ ERROR ]: Caught exception:

File: src/core/id/NamedAtomID_Map.hh:390
Residue outside res_map range

AN INTERNAL ERROR HAS OCCURED. PLEASE SEE THE CONTENTS OF ROSETTA_CRASH.log FOR DETAILS.

---------------------------------------------------------------
[ ERROR ]: Error(s) were encountered when running jobs.
1 jobs failed;
Check the output further up for additional error messages.
---------------------------------------------------------------

Attachment	Size
01-MD-086DS.pdb	440.28 KB
DHD.params	4.11 KB
flags2	321 bytes

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Post Situation:

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Applying dihedral constraints to TRP dipeptide minimization. ACE/NME termni.

reoverstreet — Mon, 11 Jul 2022 21:39:18 +0000

I have been attempting to apply dihedral constraints to the phi/psi angles of a small TRP dipeptide minimization without success. From the output pdb it appears the second dihedral constraint is not applied to the CN atom of the Acetylayted end cap. This dihedral angle shifts to 150 degrees despite a very strong constraint. I suspect Rosetta might be selecting the first CN atom it finds which would be the methyl carbon on the NME cap rather than the carbonyl carbon on the ACE group of the same name.

My main goal here is to interpolate the 2D psi/phi potential energy surface for different canonical and non-canonical residues for comparison. For this I'll be applying dihedral constraints across the phi/psi grid, minimizing each point, then calculating a static score with any constraints removed.

I am using the linux_2020.08.61146_bundle with precompiled binaries.

Any help would be greatly appreciated.

PDB File (attached):

Constraints File: (This is a test case to try and fix dihedral angles)

Dihedral CN 1 N 1 CA 1 C 1 HARMONIC -3.14 0.05
Dihedral N 1 CA 1 C 1 NM 1 HARMONIC -3.14 0.05

Input flags:

-s pes.pdb
-run:min_type lbfgs_armijo_nonmonotone_atol
-run:min_tolerance 0.00000001
-constraints:cst_file cstfile
-score:weights ref2015_cst
-out:suffix _minwithcsts
-optimization:default_max_cycles 1000000000

Attachment	Size
TRP Dipeptide	5.48 KB
rosetta output	9.16 KB
output pdb	7.29 KB

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Post Situation:

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Chemically Modified Residues

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

Forums:

Post Situation:

constraining different chains together in rosetta_cm

y_atsmonraz — Thu, 18 Nov 2021 10:59:29 +0000

Hi everyone,

I am trying to construct a homology model with 4 chains, the primary one (A) being a protein and the 3 others being an RNA chain and two DNA chains.. However, when the hybridize mover starts to build the model via rosetta_scripts it throws out the nucleotide chains from the protein while I know that they should be inserted into it so I tried using constrains as suggested in the constraints guide for rosetta cm as well as using the pdb specific labels for constrains as described here in the forums but for some reason my pose includes only the protein residues without anyone of. the nucleotide chains. Originally, I threaded the full 4 chains with partial thread while leaving the nucleotides as they are in the template, and adding the nuc. chains into the fasta and alignment which seemed to work. However, apparently they're missing in the pose so I'm obviously doing something wrong.

Thanks in advance for any responses on this matter,

Category:

Forums:

Rosetta 3 - Applications

Post Situation:

calcium metal nomenclature: Rosetta_cm confusing HETATM CA (calcium) with ATOM CA (alpha-carbon)

rlwoltz — Wed, 04 Aug 2021 06:26:29 +0000

Dear community,

I had this posted under a different sub-forum but I realized it didn't fit that forum so deleted it and reposting here.

Hopefully this is a simple answer but I couldn't find any answer and I don't remember this happening on a previous rosetta version, just updated from 2019 to 2021.16.61629_bundle. The goal is to add constraints to the amino acids that bind calcium in a homology model since they are in a small loop and can reorient without calcium present. I'm using the metal_setup mover to apply constraints but I'm open to other suggestions.

I'm doing a homology model of a 4-unit symmetrical membrane channel coupled with Calmodulin. The channel and Calmodulin are seperate chains which is denoted in the fasta with a "/" in the sequence to show the split. All this works fine for un-calcified calmodulin. However, now I'm making a calcified calmodulin structure and I have calcium ions in the single unit INPUT.pdb (output of make_symm.sh file. The thread is made with no issue. The problem is the next step of using rosetta_CM and the xml. I'm using the metals setup mover line (1) to denote the amino acids and residues. However, the calcium ions are being confused by roestta for Alpha-Carbons. I have three Calciums per subunit and they are all being overlayed onto the last alpha carbon in the protein sequence for each single unit (2).

Is there a special residue or atom name the rosetta is expecting for Calciums? currently the only naming scheme that works is "CA". (3)

Thanks for any help and let me know if you need any more information,

Ryan

1. calcium is residues 526-528. interacting residues is 397-408 --> 526, 433-433 --> 527, 470-480 --> 528

2. notice that the Calciums have the same coordinates as the first alpha-carbon of chain B the start of calmodulin. this is true for all 4 symmetrical units

ATOM 6185 OD1 ASN A 379 -2.989 8.407 56.731 1.00 0.00 O
ATOM 6186 ND2 ASN A 379 -3.678 8.654 54.615 1.00 0.00 N
ATOM 6187 H ASN A 379 -5.605 5.733 55.922 1.00 0.00 H
ATOM 6188 HA ASN A 379 -4.757 7.483 58.184 1.00 0.00 H
ATOM 6189 1HB ASN A 379 -5.936 8.097 55.462 1.00 0.00 H
ATOM 6190 2HB ASN A 379 -5.666 9.317 56.708 1.00 0.00 H
ATOM 6191 1HD2 ASN A 379 -2.719 8.727 54.264 1.00 0.00 H
ATOM 6192 2HD2 ASN A 379 -4.442 8.704 53.978 1.00 0.00 H
TER
ATOM 6194 N ASP B 380 -1.237 -47.247 33.849 1.00 0.00 N
ATOM 6195 CA ASP B 380 -2.006 -46.260 34.601 1.00 0.00 C
ATOM 6196 C ASP B 380 -2.779 -45.354 33.619 1.00 0.00 C
ATOM 6197 O ASP B 380 -3.335 -45.841 32.634 1.00 0.00 O
ATOM 6198 CB ASP B 380 -1.035 -45.467 35.514 1.00 0.00 C
ATOM 6199 CG ASP B 380 -1.668 -44.574 36.608 1.00 0.00 C
ATOM 6200 OD1 ASP B 380 -2.103 -44.975 37.659 1.00 0.00 O
...

HETATM 8425 CA CA C 526 -2.006 -46.260 34.601 1.00 0.00 CA
HETATM 8426 CA CA C 527 -2.006 -46.260 34.601 1.00 0.00 CA
HETATM 8427 CA CA C 528 -2.006 -46.260 34.601 1.00 0.00 CA

3. last few lines of input file. notice no TER line although I've tried it with. notice different XYZ coordinates for all atoms. I've also tried adjusting the spacing of the "CA" in the residue column. Calmodulin for the input as chain A but converted to chain B due to the fasta file input described above.

ATOM 5840 CA ASP A 380 -5.804 -51.544 37.679 1.00 0.00 C
...

ATOM 8068 3HB ALA A 525 -34.729 -39.328 36.187 1.00 0.00 H
HETATM 8069 CA CA A 526 2.182 -32.441 49.215 1.00239.49
HETATM 8070 CA CA A 527 -8.813 -37.633 50.564 1.00182.89
HETATM 8071 CA CA A 528 -33.639 -23.142 47.008 1.00223.54

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Post Situation:

FlexPepDock bug? Constraints do not appear in total_score?

nrollins — Mon, 26 Jul 2021 21:29:26 +0000

Hi, looking for some help,

It appears that constraints do not contribute to the final score output when running the FlexPepDock ab initio protocol.

I am getting docking samples that should yield score penalties >1000 under the provided distance constraints (AtomPair FLAT_HARMONIC). However, the scorefile reports numbers consistent with the score absent of penalties (approx -550, for a protein length 300 and peptide length 5).

I provide the constraints file with the flag -constraints:cst_file

Does anyone have experience with this? How have you set up constraints in your FlexPepDock runs, and can you confirm the constraints impacted the score?

Thank you!

Nathan

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Forums:

Rosetta 3 - Applications

Post Situation:

Loop modeling with constraints

agctomer — Sat, 20 Mar 2021 10:53:26 +0000

Hi,

I am trying to model a loop with a constraints file (the constraints are for the atoms of the loop).

but every time I get this message:

[FILE]: src/core/pose/util.cc
[LINE]: 704
[START_MESSAGE]
Atom 'OVL1 31' not found

[END_MESSAGE]
[END_CRASH_REPORT]

I also tried to set the flag "-constraints:named" to true but it didn't help...

I am using the following command:

loopmodel.linuxgccrelease -ex1 -ex2 -extrachi_cutoff 0 -loops:remodel perturb_kic -loops:refine refine_kic -constraints:named true -loops:fix_natsc -in:file:fullatom -in:file:s my_file.pdb -loops:loop_file my_loop_file -nstruct 1 -constraints:cst:file my_const -constraints:cst_weight 1.0 > loop_model.log

Is there any way to model a loop in rosetta with a constraints file (without constraints it work fine)?

thanks!

Category:

Loop Modeling

Forums:

Rosetta 3 - Applications

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