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dssp-broken pipe error
- cvieira
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7 years 8 months ago #5794
by cvieira
dssp-broken pipe error was created by cvieira
Hi,
I am trying to create a CG model for the 3HUS.pdb file, however, it gives me this error overtime I try to run martinize.py
python martinize.py -f 3HUS.pdb -o system.top -x 3HUS-CG.pdb -dssp ./mkdssp -p backbone -ff martini22
Traceback (most recent call last):
File "martinize.py", line 4792, in <module>
main(options)
File "martinize.py", line 4480, in main
ss += chain.dss(method, executable)
File "martinize.py", line 3289, in dss
self.set_ss(ssDetermination[method](self, atomlist, executable), source=method)
File "martinize.py", line 2654, in call_dssp
for line in open(ssdfile).readlines():
IOError: [Errno 2] No such file or directory: 'chain_B.ssd'
I give the correct path to the dssp executable, however, it seems that I have something missing. I also tried using -dssp ./3HUS.dssp but its says: a problem occurred when calling ./3HUS.dssp. Do I need to create a .ssd file. If so, any ideas on how to I do it? Do I create the .ssd files using the GROMACS environment?
Thank you for any help
I am trying to create a CG model for the 3HUS.pdb file, however, it gives me this error overtime I try to run martinize.py
python martinize.py -f 3HUS.pdb -o system.top -x 3HUS-CG.pdb -dssp ./mkdssp -p backbone -ff martini22
Traceback (most recent call last):
File "martinize.py", line 4792, in <module>
main(options)
File "martinize.py", line 4480, in main
ss += chain.dss(method, executable)
File "martinize.py", line 3289, in dss
self.set_ss(ssDetermination[method](self, atomlist, executable), source=method)
File "martinize.py", line 2654, in call_dssp
for line in open(ssdfile).readlines():
IOError: [Errno 2] No such file or directory: 'chain_B.ssd'
I give the correct path to the dssp executable, however, it seems that I have something missing. I also tried using -dssp ./3HUS.dssp but its says: a problem occurred when calling ./3HUS.dssp. Do I need to create a .ssd file. If so, any ideas on how to I do it? Do I create the .ssd files using the GROMACS environment?
Thank you for any help
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- xavier
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7 years 7 months ago #5836
by xavier
Replied by xavier on topic dssp-broken pipe error
The error does not relate to dssp but to that you seem to have two chains and the program seems to have trouble dealing with chain B ... try decomposing the chains in the pdb and/or clean up the pdf file.
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- cvieira
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7 years 6 months ago #5908
by cvieira
Replied by cvieira on topic dssp-broken pipe error
Hi,
Thank you for your response. What I did was, instead of using the -dssp flag, I used the -ss and inputed the .dssp file directly:
python martinize.py -f 3HUS.pdb -o system.top -x 3HUS-CG.pdb -ss 3HUS.dssp -ff martini22
And that seemed to work. The problem is that after I run the whole simulation, I try to create a graph of the RMSD in the backbone, but I consistently get 0 elements in the backbone, and when I choose the backbone option to graph it says that it needs three or more points to fit (because apparently no atoms were placed in the backbone)?
Can this have to do with dssp? If not, has this problem ever been encountered.
Any help on how I can solve this problem will be much appreciated.
Best,
Christina
Thank you for your response. What I did was, instead of using the -dssp flag, I used the -ss and inputed the .dssp file directly:
python martinize.py -f 3HUS.pdb -o system.top -x 3HUS-CG.pdb -ss 3HUS.dssp -ff martini22
And that seemed to work. The problem is that after I run the whole simulation, I try to create a graph of the RMSD in the backbone, but I consistently get 0 elements in the backbone, and when I choose the backbone option to graph it says that it needs three or more points to fit (because apparently no atoms were placed in the backbone)?
Can this have to do with dssp? If not, has this problem ever been encountered.
Any help on how I can solve this problem will be much appreciated.
Best,
Christina
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- peterkroon
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7 years 6 months ago #5910
by peterkroon
Replied by peterkroon on topic dssp-broken pipe error
DSSP does not know the Martini representation of a protein. Furthermore, the atoms that define the ramachandran angles no longer exist, so DSSP will be *completely* lost, even if you rename the backbone beads to something recognizable. You could try backmapping your simulation to atomistic, and go from there. But that would not make sense - in Martini the secondary is fixed by either an elastic network, or extended dihedrals. So something that starts as a helix will always remain a helix.
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- cvieira
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7 years 6 months ago #5914
by cvieira
Replied by cvieira on topic dssp-broken pipe error
Hi,
I am trying to simulate 1HEL lysozyme, without using elastic network constraints. I also would not prefer to use a extended dihedral constraint as I am trying to duplicate the results of a paper which specifically says that they did not use any of the constraints I mentioned. When I perform the simulation following the commands in the protein tutorial, I always get 0 elements in the backbone. I tried to manually add the number of backbone beads by creating an index file, and inputing the index file after I solvate the system and start the first energy minimization step. This method that I used did not work, and I continue to get 0 backbone elements.
Does the secondary structure of the CG protein have to be fixed with either elastic network or extended dihedrals in the beginning? If yes, not using any of those constraints will result in 0 elements in the backbone? If I have to use one of the constratinst, how can I use the extended dihedrals in my command? I know I can use -ed, but I am not sure what parameters I have to specify after the ed flag. If not, how can I fix my system so that it recognizes residues that are supposed to be in the backbone?
Thank you for your time.
I am trying to simulate 1HEL lysozyme, without using elastic network constraints. I also would not prefer to use a extended dihedral constraint as I am trying to duplicate the results of a paper which specifically says that they did not use any of the constraints I mentioned. When I perform the simulation following the commands in the protein tutorial, I always get 0 elements in the backbone. I tried to manually add the number of backbone beads by creating an index file, and inputing the index file after I solvate the system and start the first energy minimization step. This method that I used did not work, and I continue to get 0 backbone elements.
Does the secondary structure of the CG protein have to be fixed with either elastic network or extended dihedrals in the beginning? If yes, not using any of those constraints will result in 0 elements in the backbone? If I have to use one of the constratinst, how can I use the extended dihedrals in my command? I know I can use -ed, but I am not sure what parameters I have to specify after the ed flag. If not, how can I fix my system so that it recognizes residues that are supposed to be in the backbone?
Thank you for your time.
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- peterkroon
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7 years 6 months ago #5916
by peterkroon
Replied by peterkroon on topic dssp-broken pipe error
Hi,
DSSP (and all gromacs related software) looks for the atoms NCOH to find "backbone elements". These no longer exist in the Martini world. You'll probably have to write your own analysis software if you want to keep going down this road.
Which tool specifically says 0 backbone elements? Can you post the exact command you use and the output you get?
The Martini protein ff was parametrized with a fixed secondary structure using either an elastic network or extended dihedrals (-ed flag, no arguments/parameters). Any simulation you run without either of these is likely to produce non-physical results - e.g. unfolding proteins. If you run martinize with no arguments in this regard (martinize.py -f 1hel.pdb -ff martini22 -o tmp.top), it will assume everything is a coil, and use parameters for those (backbone angle, dihedral terms and beadtypes). I find it highly unlikely this is what you want.
DSSP (and all gromacs related software) looks for the atoms NCOH to find "backbone elements". These no longer exist in the Martini world. You'll probably have to write your own analysis software if you want to keep going down this road.
Which tool specifically says 0 backbone elements? Can you post the exact command you use and the output you get?
The Martini protein ff was parametrized with a fixed secondary structure using either an elastic network or extended dihedrals (-ed flag, no arguments/parameters). Any simulation you run without either of these is likely to produce non-physical results - e.g. unfolding proteins. If you run martinize with no arguments in this regard (martinize.py -f 1hel.pdb -ff martini22 -o tmp.top), it will assume everything is a coil, and use parameters for those (backbone angle, dihedral terms and beadtypes). I find it highly unlikely this is what you want.
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- cvieira
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7 years 6 months ago #5917
by cvieira
Replied by cvieira on topic dssp-broken pipe error
Hi,
Thank you for your last response. I see that I have 0 elements whenever I am trying to plot an RMSD and also when I create an index file, there is no atoms under backbone:
This is what I get when using trjconv in order to plot a backbone RMSD:
Will write xtc: Compressed trajectory (portable xdr format)
Reading file test3.tpr, VERSION 4.6.1 (single precision)
Reading file test3.tpr, VERSION 4.6.1 (single precision)
Select group for output
Group 0 ( System) has 8281 elements
Group 1 ( Protein) has 283 elements
Group 2 ( Protein-H) has 283 elements
Group 3 ( C-alpha) has 0 elements
Group 4 ( Backbone) has 0 elements
Group 5 ( MainChain) has 0 elements
Group 6 ( MainChain+Cb) has 0 elements
Group 7 ( MainChain+H) has 0 elements
Group 8 ( SideChain) has 283 elements
Group 9 ( SideChain-H) has 283 elements
Group 10 ( Prot-Masses) has 283 elements
Group 11 ( non-Protein) has 7998 elements
Group 12 ( Water) has 7998 elements
Group 13 ( SOL) has 7998 elements
Group 14 ( non-Water) has 283 elements
Select a group: 0
Selected 0: 'System'
Reading frame 0 time 0.000
Precision of test3.xtc is 0.01 (nm)
Using output precision of 0.001 (nm)
Last frame 0 time 0.000
Thank you for your last response. I see that I have 0 elements whenever I am trying to plot an RMSD and also when I create an index file, there is no atoms under backbone:
This is what I get when using trjconv in order to plot a backbone RMSD:
Will write xtc: Compressed trajectory (portable xdr format)
Reading file test3.tpr, VERSION 4.6.1 (single precision)
Reading file test3.tpr, VERSION 4.6.1 (single precision)
Select group for output
Group 0 ( System) has 8281 elements
Group 1 ( Protein) has 283 elements
Group 2 ( Protein-H) has 283 elements
Group 3 ( C-alpha) has 0 elements
Group 4 ( Backbone) has 0 elements
Group 5 ( MainChain) has 0 elements
Group 6 ( MainChain+Cb) has 0 elements
Group 7 ( MainChain+H) has 0 elements
Group 8 ( SideChain) has 283 elements
Group 9 ( SideChain-H) has 283 elements
Group 10 ( Prot-Masses) has 283 elements
Group 11 ( non-Protein) has 7998 elements
Group 12 ( Water) has 7998 elements
Group 13 ( SOL) has 7998 elements
Group 14 ( non-Water) has 283 elements
Select a group: 0
Selected 0: 'System'
Reading frame 0 time 0.000
Precision of test3.xtc is 0.01 (nm)
Using output precision of 0.001 (nm)
Last frame 0 time 0.000
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- peterkroon
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7 years 6 months ago #5919
by peterkroon
Replied by peterkroon on topic dssp-broken pipe error
Right. This has the same reason as posted earlier. Make an index file (gmx make_ndx) containing all beads with name 'BB', and feed that to gmx rmsd (or trjconv) with the -n flag. You may have to call the group something different than Backbone though.
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