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Structure file generation for PEGylated oligopeptides with Martini3
- antabear
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1 year 7 months ago #9491
by antabear
Structure file generation for PEGylated oligopeptides with Martini3 was created by antabear
Hello,
I would like to generate a structure file for PEGylated oligopeptides followed by the protocol attached below.
pubmed.ncbi.nlm.nih.gov/33125658/
I converted an AA structure pdb file to a CG itp file using martinize 2 and tried to link the peptide to PEG chain, but IOError was raised.
IOError(MultiblockError.format(meta_molecule.nodes[start_node]["resname"])
OSError: Block molecule_0 seems to represent more than a single residue,
but within the residue graph only a single corresponding node
was found. If you have blocks representing multiresidues
provide the full residue graph and label all nodes that
corresponding to multiresidues with the "from_itp" label.
Which structure file should I change to fix the problem?
Thanks in advance.
Best,
Kim
I would like to generate a structure file for PEGylated oligopeptides followed by the protocol attached below.
pubmed.ncbi.nlm.nih.gov/33125658/
I converted an AA structure pdb file to a CG itp file using martinize 2 and tried to link the peptide to PEG chain, but IOError was raised.
IOError(MultiblockError.format(meta_molecule.nodes[start_node]["resname"])
OSError: Block molecule_0 seems to represent more than a single residue,
but within the residue graph only a single corresponding node
was found. If you have blocks representing multiresidues
provide the full residue graph and label all nodes that
corresponding to multiresidues with the "from_itp" label.
Which structure file should I change to fix the problem?
Thanks in advance.
Best,
Kim
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- fgrunewald
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1 year 7 months ago #9493
by fgrunewald
Replied by fgrunewald on topic Structure file generation for PEGylated oligopeptides with Martini3
Hi Kim,
The problem is that the tutorial/protocol is out of date with the most recent polyply version. Have a look here at this discussion for the new workflow:
github.com/marrink-lab/polyply_1.0/discussions/261?converting=1
If this doesn't solve your problem or you still have persisting issues feel free to simply post under the discussion thread on GitHub. Getting an answer on GitHub is typically faster than here on the Forum.
Cheers,
Fabian
The problem is that the tutorial/protocol is out of date with the most recent polyply version. Have a look here at this discussion for the new workflow:
github.com/marrink-lab/polyply_1.0/discussions/261?converting=1
If this doesn't solve your problem or you still have persisting issues feel free to simply post under the discussion thread on GitHub. Getting an answer on GitHub is typically faster than here on the Forum.
Cheers,
Fabian
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- antabear
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1 year 7 months ago #9498
by antabear
Replied by antabear on topic Structure file generation for PEGylated oligopeptides with Martini3
Hello Fabian,
The problem is solved and I got the itp file for the PEGylated peptide.
BUT I could not translate the itp file to gro file. Some beads name for amino acids does not exist in 'martini_v3.0.0.ifp' file, so I should've changed them.
Here I attached the error with the command. Do you also have any new updates with 'gen_coords'?
polyply gen_coords -p system.top -o pepPEG.gro -name pepPEG -c pep_cg.gro -box 20 20 20
INFO - step - reading topology
INFO - step - processing topology
INFO - step - loading coordinates
INFO - step - checking residue integrity
INFO - step - generating templates
0%| | 0/300 [00:00<?, ?it/s]
Traceback (most recent call last):
File "/Users/nai/dhwanit/.local/bin/polyply", line 256, in <module>
main()
File "/Users/nai/dhwanit/.local/bin/polyply", line 252, in main
args.func(args)
File "/Users/nai/dhwanit/.local/lib/python3.8/site-packages/polyply/src/gen_coords.py", line 135, in gen_coords
GenerateTemplates(topology=topology, max_opt=10).run_system(topology)
File "/Users/nai/dhwanit/.local/lib/python3.8/site-packages/polyply/src/processor.py", line 31, in run_system
mols.append(self.run_molecule(molecule))
File "/Users/nai/dhwanit/.local/lib/python3.8/site-packages/polyply/src/generate_templates.py", line 364, in run_molecule
templates, volumes = self._gen_templates(meta_molecule)
File "/Users/nai/dhwanit/.local/lib/python3.8/site-packages/polyply/src/generate_templates.py", line 353, in _gen_templates
self.volumes[resname] = compute_volume(meta_molecule, block, coords, self.topology.nonbond_params)
File "/Users/nai/dhwanit/.local/lib/python3.8/site-packages/polyply/src/generate_templates.py", line 189, in compute_volume
radgyr = radius_of_gyration(geom_vects)
File "/usr/lib/python3/dist-packages/numba/dispatcher.py", line 401, in _compile_for_args
error_rewrite(e, 'typing')
File "/usr/lib/python3/dist-packages/numba/dispatcher.py", line 344, in error_rewrite
reraise(type(e), e, None)
File "/usr/lib/python3/dist-packages/numba/six.py", line 668, in reraise
raise value.with_traceback(tb)
numba.errors.TypingError: Failed in nopython mode pipeline (step: nopython frontend)
Direct iteration is not supported for arrays with dimension > 1. Try using indexing instead.
[1] During: typing of intrinsic-call at /Users/nai/dhwanit/.local/lib/python3.8/site-packages/polyply/src/linalg_functions.py (163)
File "../../../.local/lib/python3.8/site-packages/polyply/src/linalg_functions.py", line 163:
def _radius_of_gyration(points):
<source elided>
count=0
for i in points:
^
The problem is solved and I got the itp file for the PEGylated peptide.
BUT I could not translate the itp file to gro file. Some beads name for amino acids does not exist in 'martini_v3.0.0.ifp' file, so I should've changed them.
Here I attached the error with the command. Do you also have any new updates with 'gen_coords'?
polyply gen_coords -p system.top -o pepPEG.gro -name pepPEG -c pep_cg.gro -box 20 20 20
INFO - step - reading topology
INFO - step - processing topology
INFO - step - loading coordinates
INFO - step - checking residue integrity
INFO - step - generating templates
0%| | 0/300 [00:00<?, ?it/s]
Traceback (most recent call last):
File "/Users/nai/dhwanit/.local/bin/polyply", line 256, in <module>
main()
File "/Users/nai/dhwanit/.local/bin/polyply", line 252, in main
args.func(args)
File "/Users/nai/dhwanit/.local/lib/python3.8/site-packages/polyply/src/gen_coords.py", line 135, in gen_coords
GenerateTemplates(topology=topology, max_opt=10).run_system(topology)
File "/Users/nai/dhwanit/.local/lib/python3.8/site-packages/polyply/src/processor.py", line 31, in run_system
mols.append(self.run_molecule(molecule))
File "/Users/nai/dhwanit/.local/lib/python3.8/site-packages/polyply/src/generate_templates.py", line 364, in run_molecule
templates, volumes = self._gen_templates(meta_molecule)
File "/Users/nai/dhwanit/.local/lib/python3.8/site-packages/polyply/src/generate_templates.py", line 353, in _gen_templates
self.volumes[resname] = compute_volume(meta_molecule, block, coords, self.topology.nonbond_params)
File "/Users/nai/dhwanit/.local/lib/python3.8/site-packages/polyply/src/generate_templates.py", line 189, in compute_volume
radgyr = radius_of_gyration(geom_vects)
File "/usr/lib/python3/dist-packages/numba/dispatcher.py", line 401, in _compile_for_args
error_rewrite(e, 'typing')
File "/usr/lib/python3/dist-packages/numba/dispatcher.py", line 344, in error_rewrite
reraise(type(e), e, None)
File "/usr/lib/python3/dist-packages/numba/six.py", line 668, in reraise
raise value.with_traceback(tb)
numba.errors.TypingError: Failed in nopython mode pipeline (step: nopython frontend)
Direct iteration is not supported for arrays with dimension > 1. Try using indexing instead.
[1] During: typing of intrinsic-call at /Users/nai/dhwanit/.local/lib/python3.8/site-packages/polyply/src/linalg_functions.py (163)
File "../../../.local/lib/python3.8/site-packages/polyply/src/linalg_functions.py", line 163:
def _radius_of_gyration(points):
<source elided>
count=0
for i in points:
^
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- fgrunewald
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1 year 7 months ago #9499
by fgrunewald
Replied by fgrunewald on topic Structure file generation for PEGylated oligopeptides with Martini3
It looks like some interactions are zero or undefined. In principle you shouldn't have to edit the interactions itp file. Please note that you cannot simply mix different Martini versions. The tutorial is build upon the martini3 beta version not the final release version.
Without knowing what you changed I cannot for certain say what caused the error. Can you provide your input setup.
Cheers,
Fabian
Without knowing what you changed I cannot for certain say what caused the error. Can you provide your input setup.
Cheers,
Fabian
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- antabear
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1 year 7 months ago #9508
by antabear
Replied by antabear on topic Structure file generation for PEGylated oligopeptides with Martini3
I tried run the simulation again with Martini3 and still got the same error.
This is the command that I used and 'polyply gen_coords' did not work for me.
$ martinize2 -f pep.pdb -o topol.top -x pep_cg.pdb -ff martini3001
$ polyply gen_seq -f molecule_0.itp -from_file protein:molecule_0 -from_string linker:1:1:MEE-1.0 polymer:50:1:PEO-1.0 end:1:1:OHend-1.0 -seq protein linker polymer end -connects 0:1:0-0 1:2:0-0 2:3:49-0 -o sequence.json -name test -label 0:"from_itp":"molecule_0-1.
$ polyply gen_itp -f molecule_0.itp MEE.itp combined_links.ff PEO.martini.3.itp OH_end.itp -seqf sequence.json -o pepPEG.itp -name pepPEG
$ gmx editconf -f pep_cg.pdb -o pep_cg.gro
$ polyply gen_coords -p system.top -o pepPEG.gro -name pepPEG -c pep_cg.gro -box 20 20 20
I used .itp file for PEO below. Is it compatible to Martini3?
[ moleculetype ]
; name nexcl.
PEO 1
;
[ atoms ]
1 SN1a 1 PEO EO 1 0.000 45
[ bonds ]
; back bone bonds
1 2 1 0.37 7000
;
[ angles ]
;
1 2 3 2 135.00 50
1 2 3 10 135.00 75
;
[ dihedrals ]
1 2 3 4 1 180.00 1.96 1
1 2 3 4 1 0 0.18 2
1 2 3 4 1 0 0.33 3
1 2 3 4 1 0 0.12 4
Best,
Kim
This is the command that I used and 'polyply gen_coords' did not work for me.
$ martinize2 -f pep.pdb -o topol.top -x pep_cg.pdb -ff martini3001
$ polyply gen_seq -f molecule_0.itp -from_file protein:molecule_0 -from_string linker:1:1:MEE-1.0 polymer:50:1:PEO-1.0 end:1:1:OHend-1.0 -seq protein linker polymer end -connects 0:1:0-0 1:2:0-0 2:3:49-0 -o sequence.json -name test -label 0:"from_itp":"molecule_0-1.
$ polyply gen_itp -f molecule_0.itp MEE.itp combined_links.ff PEO.martini.3.itp OH_end.itp -seqf sequence.json -o pepPEG.itp -name pepPEG
$ gmx editconf -f pep_cg.pdb -o pep_cg.gro
$ polyply gen_coords -p system.top -o pepPEG.gro -name pepPEG -c pep_cg.gro -box 20 20 20
I used .itp file for PEO below. Is it compatible to Martini3?
[ moleculetype ]
; name nexcl.
PEO 1
;
[ atoms ]
1 SN1a 1 PEO EO 1 0.000 45
[ bonds ]
; back bone bonds
1 2 1 0.37 7000
;
[ angles ]
;
1 2 3 2 135.00 50
1 2 3 10 135.00 75
;
[ dihedrals ]
1 2 3 4 1 180.00 1.96 1
1 2 3 4 1 0 0.18 2
1 2 3 4 1 0 0.33 3
1 2 3 4 1 0 0.12 4
Best,
Kim
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