Error when running prepack of PLEXPEPDOCKING

[Anonymous]

Hello everyone!
I use Plexpepdocking (Rosetta 3.4), in my structure have one ion Zn , but Plexpepdock can not recognize it.
Please take a look on my pdb file and tell me how to fix this Error.
Thank you so much for your help.

Thank!!!

this is the flag for pre_packing
-s tryzn.pdb
-database /home/tuongvy/SW/rosetta3.4/rosetta_database

-flexpep_prepack
-ex1
-ex2aro

This is the ERROR

ERROR: unknown atom_name: ZN CA
ERROR:: Exit from: src/core/chemical/ResidueType.cc line: 1692

[Anonymous]

THIS IS THE ERROR I GET (sorry for mistake at written error above)

[node5:26644] *** Process received signal ***
[node5:26644] Signal: Segmentation fault (11)
[node5:26644] Signal code: Address not mapped (1)
[node5:26644] Failing at address: (nil)
[node5:26644] [ 0] /lib64/libpthread.so.0[0x393220f710]
[node5:26644] [ 1] /home/tuongvy/SW/rosetta3.4/rosetta_source/build/src/release/linux/2.6/64/x86/gcc/4.1/mpi/libcore.2.so(_ZNK4core12conformation12Conformation28backbone_torsion_angle_atomsERKNS_2id9TorsionIDERNS2_6AtomIDES7_S7_S7_+0x155f)[0x7f1ec947d79f]
[node5:26644] [ 2] /home/tuongvy/SW/rosetta3.4/rosetta_source/build/src/release/linux/2.6/64/x86/gcc/4.1/mpi/libcore.2.so(_ZNK4core12conformation12Conformation26get_torsion_angle_atom_idsERKNS_2id9TorsionIDERNS2_6AtomIDES7_S7_S7_+0x1a2)[0x7f1ec947e712]
[node5:26644] [ 3] /home/tuongvy/SW/rosetta3.4/rosetta_source/build/src/release/linux/2.6/64/x86/gcc/4.1/mpi/libcore.2.so(_ZNK4core12conformation12Conformation17atom_tree_torsionERKNS_2id9TorsionIDE+0x9a)[0x7f1ec947e93a]
[node5:26644] [ 4] /home/tuongvy/SW/rosetta3.4/rosetta_source/build/src/release/linux/2.6/64/x86/gcc/4.1/mpi/libcore.2.so(_ZNK4core12conformation12Conformation23update_residue_torsionsEmb+0x117)[0x7f1ec947eac7]
[node5:26644] [ 5] /home/tuongvy/SW/rosetta3.4/rosetta_source/build/src/release/linux/2.6/64/x86/gcc/4.1/mpi/libcore.2.so(_ZNK4core12conformation12Conformation23update_residue_torsionsEv+0x1a5)[0x7f1ec947f045]
[node5:26644] [ 6] /home/tuongvy/SW/rosetta3.4/rosetta_source/build/src/release/linux/2.6/64/x86/gcc/4.1/mpi/libcore.2.so(_ZN4core12conformation12Conformation15setup_atom_treeEv+0xa4)[0x7f1ec947f2a4]
[node5:26644] [ 7] /home/tuongvy/SW/rosetta3.4/rosetta_source/build/src/release/linux/2.6/64/x86/gcc/4.1/mpi/libcore.2.so(_ZN4core12conformation12Conformation9fold_treeERKNS_10kinematics8FoldTreeE+0x6ac)[0x7f1ec9480c8c]
[node5:26644] [ 8] /home/tuongvy/SW/rosetta3.4/rosetta_source/build/src/release/linux/2.6/64/x86/gcc/4.1/mpi/libprotocols_c.5.so(_ZN9protocols15flexpep_docking22FlexPepDockingProtocol14setup_foldtreeERN4core4pose4PoseE+0xd3d)[0x7f1ecf8cc77d]
[node5:26644] [ 9] /home/tuongvy/SW/rosetta3.4/rosetta_source/build/src/release/linux/2.6/64/x86/gcc/4.1/mpi/libprotocols_c.5.so(_ZN9protocols15flexpep_docking22FlexPepDockingProtocol5applyERN4core4pose4PoseE+0xb9)[0x7f1ecf8d9bf9]
[node5:26644] [10] /home/tuongvy/SW/rosetta3.4/rosetta_source/build/src/release/linux/2.6/64/x86/gcc/4.1/mpi/libprotocols.1.so(_ZN9protocols3jd214JobDistributor7go_mainEN7utility7pointer10owning_ptrINS_5moves5MoverEEE+0xffc)[0x7f1ecb7e820c]
[node5:26644] [11] /home/tuongvy/SW/rosetta3.4/rosetta_source/build/src/release/linux/2.6/64/x86/gcc/4.1/mpi/libprotocols.1.so(_ZN9protocols3jd225MPIWorkPoolJobDistributor8slave_goEN7utility7pointer10owning_ptrINS_5moves5MoverEEE+0x48)[0x7f1ecb80a7e8]
[node5:26644] [12] /home/tuongvy/SW/rosetta3.4/rosetta_source/build/src/release/linux/2.6/64/x86/gcc/4.1/mpi/libprotocols.1.so(_ZN9protocols3jd225MPIWorkPoolJobDistributor2goEN7utility7pointer10owning_ptrINS_5moves5MoverEEE+0x96)[0x7f1ecb808376]
[node5:26644] [13] /home/tuongvy/SW/rosetta3.4/rosetta_source/bin/FlexPepDocking.mpi.linuxgccrelease(main+0x2e6)[0x40af36]
[node5:26644] [14] /lib64/libc.so.6(__libc_start_main+0xfd)[0x3931e1ed1d]
[node5:26644] [15] /home/tuongvy/SW/rosetta3.4/rosetta_source/bin/FlexPepDocking.mpi.linuxgccrelease[0x40ab59]
[node5:26644] *** End of error message ***

[Anonymous]

Hi,
The protocol is actually called FlexPepDock.
Regarding the metal ion issue, the protocol can’t handle metal ions right now, but this feature will be implemented in future.
For now I will advice to delete the metal ion from the pdb and then running prepacking. And also remember FlexPepDock always assumes second chain in the pdb as the peptide chain and first chain as receptor unless explicitly mention using flags.
best,

[Anonymous]

Select top scoring decoy from your each run and compare the scores. Native orientation is expected to have lower score. Also look how structurally conserved the residues are in different runs. I will advice to use -unboundrot receptor.pdb flag to add the receptor side chains to the rotamer library.

[Anonymous]

-unboundrot flag add the position-specific rotamers of the specified structure to the rotamer library (usually used to include rotamers of unbound receptor). This helps to use receptor rotamer during the run.
By default FlexPepDock assumes the first chain as the receptor. Receptor BB sampling might have happened because of that. you can use -receptor_chain flag to mention chain explicitly. Have you notice significant difference in energy in different runs? That will be first criteria to narrow down candidate for native. I can put the idea of being structurally conserved in another way by saying that for near native run you are expected to get larger cluster of decoys.

[Anonymous]

Rosetta uses monte carlo sampling to sample the conformational space. A significant amount of sampling is required to reach to the near native conformation. why should every decoy have same energy? Different decoy have different conformation resulting in different molecular interactions. Low scoring decoys are most probable candidates for near native conformation. That’s why you should analyze low scoring decoys of each run and compare them.

[Anonymous]

Thanks for your help nawsad,
When I remove Zn, I can run FlexPepDock (I do this job a week ago)
My receptor (enzyme have a mouth) and I move peptide slowly (3 Anstrong, example {0 0 3} {3 0 0} { 0 3 0} ) on this mouth and I run FlexpepDock all 200 times.
I want to find where is the binding site of this peptide on enzyme. What should I do after running. I see a score.sc table.

this is my flags for run Flexpepdock
-s 2_0001.pdb
-database /home/tuongvy/SW/rosetta3.4/rosetta_database

#-out:file:silent decoys.silent
-out:file:silent_struct_type binary

-lowres_preoptimize
-pep_refine
-rep_ramp_cycles 10
-ex1
-ex2aro
-use_input_sc
-nstruct 200

Thank you so much!!!

[Anonymous]

Thank you so much nawsad,
I want to ask some more questions, please help me.
1/Can you explain more about the flag ” -unboundrot receptor.pdb” . I confuse how to use it because I do not know anything about the biding site of peptide on its receptor.
2/I ran Plexpepdock with receptor have 2 chains (enzyme and its substrate, I set them same chain name) and peptide (this is a inhibitor follow non competitive mechanism) . After take a look on the result, I see the substrate was change its backbone). what I can do to fix this problem.
3/ I took a look on structures after running and saw that backbone of peptide change in different run. What you mean when you said “how structurally conserved the residues are in different runs”. Can you explain more? I am a new user . Can you help me more?

Thank you so much
Tuong Vy

[Anonymous]

Dear nawsad,
Now I understand about -unboundrot flag.
I see the difference in total score of each runs. But, problem is some structures have near score, the different between candidates for native (lowest score) is not significant.
I have problem about analysis the result. My professor ask me have to explain how the score each decoys different, why this decoys have high score , why that one have lower score…I take a look many decoys have significant score after running, but I can not explain. Some score have many hydrogen bonds with enzyme also have high score, and the position binding site between lower and higher score is not different so much. I think I can not cluster the decoys by score . just 1 run, the score is total different. My professor want I can divide this area on enzyme will have high score, that are will have lower score.

Can you give me advice nawsad?
what can I do?

Thank you so muc nawsad

[Anonymous]

” Different decoy have different conformation resulting in different molecular interactions”, I understand about this.
Example, with run 1st , i get the lowest score is -500, lowest score of run 2rd is -700 and lowest score of run 3 is -900… Nawsad, Can you explain more about what score I need i focus on? I think I should focus on the lowest score between low score. in my mind , I analyze run 3 with the lowest score -900 , -899,… (and analyze the decoys have score around -900 )

Thank you so much for your help!

Thank.

[Anonymous]

Hi Nawsad

I am looking for your guidance in running FlexPepdock ab initio tutorial. Is it possible to get the tutorial material so that I can try to run it. However, I have difficult to download nr database as the script always fails to download. How could I generate fragment files if make_fragment.pl does not work?

 

kind regards

Mustafa

[Anonymous]

You’re right. Analyze decoys generated in run 3. You can cluster them too and select representative from different clusters and have a close look at them.

[Author]

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