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Problem using martinize.py
- Rajat Desikan
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12 years 5 months ago #822
by Rajat Desikan
Problem using martinize.py was created by Rajat Desikan
Hi
I am trying out the protein tutorial with a different protein (!QOY.pdb). I am getting the following error. Please help. Thanks
./martinize.py -f 1QOY.pdb -o clya.top -x cg_1QOY.pdb -dssp /home/newgromacs/apps/gromacs/bin/dssp-2 -p backbone
INFO Chain termini will be charged
INFO Residues at chain brakes will not be charged
INFO Local elastic bonds will be used for extended regions.
INFO Position restraints will be generated.
WARNING Position restraints are only enabled if -DPOSRES is set in the MDP file
INFO Read input structure from file.
INFO Input structure is a PDB file.
INFO Found 3 chains:
INFO 1: A (Protein), 2371 atoms in 303 residues.
INFO 2: A (Unknown), 5 atoms in 1 residues.
INFO 3: A (Water), 339 atoms in 339 residues.
INFO Removing HETATM chain A consisting of 1 residues.
INFO Removing 339 water molecules (chain A).
INFO Merges:
INFO Total size of the system: 303 residues.
sh: /home/newgromacs/apps/gromacs/bin/: is a directory
Traceback (most recent call last):
File "./martinize.py", line 2152, in ?
ss += chain.dss(method, executable)
File "./martinize.py", line 1160, in dss
self.set_ss(ssDetermination[method](self,atomlist,executable),source=method)
File "./martinize.py", line 1336, in call_dssp
p = subp.Popen([executable,"-i","/dev/stdin","-o",ssdfile],stderr=subp.PIPE,stdout=subp.PIPE,stdin=subp.PIPE)
File "/usr/lib64/python2.4/subprocess.py", line 542, in __init__
errread, errwrite)
File "/usr/lib64/python2.4/subprocess.py", line 975, in _execute_child
raise child_exception
OSError: [Errno 13] Permission denied
I am trying out the protein tutorial with a different protein (!QOY.pdb). I am getting the following error. Please help. Thanks
./martinize.py -f 1QOY.pdb -o clya.top -x cg_1QOY.pdb -dssp /home/newgromacs/apps/gromacs/bin/dssp-2 -p backbone
INFO Chain termini will be charged
INFO Residues at chain brakes will not be charged
INFO Local elastic bonds will be used for extended regions.
INFO Position restraints will be generated.
WARNING Position restraints are only enabled if -DPOSRES is set in the MDP file
INFO Read input structure from file.
INFO Input structure is a PDB file.
INFO Found 3 chains:
INFO 1: A (Protein), 2371 atoms in 303 residues.
INFO 2: A (Unknown), 5 atoms in 1 residues.
INFO 3: A (Water), 339 atoms in 339 residues.
INFO Removing HETATM chain A consisting of 1 residues.
INFO Removing 339 water molecules (chain A).
INFO Merges:
INFO Total size of the system: 303 residues.
sh: /home/newgromacs/apps/gromacs/bin/: is a directory
Traceback (most recent call last):
File "./martinize.py", line 2152, in ?
ss += chain.dss(method, executable)
File "./martinize.py", line 1160, in dss
self.set_ss(ssDetermination[method](self,atomlist,executable),source=method)
File "./martinize.py", line 1336, in call_dssp
p = subp.Popen([executable,"-i","/dev/stdin","-o",ssdfile],stderr=subp.PIPE,stdout=subp.PIPE,stdin=subp.PIPE)
File "/usr/lib64/python2.4/subprocess.py", line 542, in __init__
errread, errwrite)
File "/usr/lib64/python2.4/subprocess.py", line 975, in _execute_child
raise child_exception
OSError: [Errno 13] Permission denied
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- Rajat Desikan
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12 years 5 months ago #823
by Rajat Desikan
Replied by Rajat Desikan on topic Problem using martinize.py
Hi
I generated the ss.dssp file separately and then used martinize.py. Now I have a new error. Please help.
./martinize.py -f 1QOY.pdb -o clya.top -x cg_1QOY.pdb -ss clya_ss.dssp -p backbone
INFO Chain termini will be charged
INFO Residues at chain brakes will not be charged
INFO Local elastic bonds will be used for extended regions.
INFO Position restraints will be generated.
WARNING Position restraints are only enabled if -DPOSRES is set in the MDP file
INFO Read input structure from file.
INFO Input structure is a PDB file.
INFO Found 3 chains:
INFO 1: A (Protein), 2371 atoms in 303 residues.
INFO 2: A (Unknown), 5 atoms in 1 residues.
INFO 3: A (Water), 339 atoms in 339 residues.
INFO Removing HETATM chain A consisting of 1 residues.
INFO Removing 339 water molecules (chain A).
INFO Merges:
INFO Total size of the system: 303 residues.
INFO Will read secondary structure from file (assuming DSSP output).
INFO Writing coarse grained structure.
INFO (Average) Secondary structure has been determined (see head of .itp-file).
Traceback (most recent call last):
File "./martinize.py", line 2328, in ?
destination.write(str(top))
File "./martinize.py", line 1656, in __str__
bonds = [str(i) for i in self.bonds["BB"]]
File "./martinize.py", line 1410, in __str__
if not self.atoms or not self.parameters or self.parameters.count(0) == len(self.parameters):
AttributeError: 'tuple' object has no attribute 'count'
I generated the ss.dssp file separately and then used martinize.py. Now I have a new error. Please help.
./martinize.py -f 1QOY.pdb -o clya.top -x cg_1QOY.pdb -ss clya_ss.dssp -p backbone
INFO Chain termini will be charged
INFO Residues at chain brakes will not be charged
INFO Local elastic bonds will be used for extended regions.
INFO Position restraints will be generated.
WARNING Position restraints are only enabled if -DPOSRES is set in the MDP file
INFO Read input structure from file.
INFO Input structure is a PDB file.
INFO Found 3 chains:
INFO 1: A (Protein), 2371 atoms in 303 residues.
INFO 2: A (Unknown), 5 atoms in 1 residues.
INFO 3: A (Water), 339 atoms in 339 residues.
INFO Removing HETATM chain A consisting of 1 residues.
INFO Removing 339 water molecules (chain A).
INFO Merges:
INFO Total size of the system: 303 residues.
INFO Will read secondary structure from file (assuming DSSP output).
INFO Writing coarse grained structure.
INFO (Average) Secondary structure has been determined (see head of .itp-file).
Traceback (most recent call last):
File "./martinize.py", line 2328, in ?
destination.write(str(top))
File "./martinize.py", line 1656, in __str__
bonds = [str(i) for i in self.bonds["BB"]]
File "./martinize.py", line 1410, in __str__
if not self.atoms or not self.parameters or self.parameters.count(0) == len(self.parameters):
AttributeError: 'tuple' object has no attribute 'count'
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- djurre
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12 years 5 months ago #824
by djurre
Replied by djurre on topic Problem using martinize.py
Hi Rajat,
I'm guessing something is wrong with the dssp2 binary. Could you try running in directly (from the commandline) on the 1QOY.py? If that doesn't work you should install/download it again.
Groetnis,
Djurre
I'm guessing something is wrong with the dssp2 binary. Could you try running in directly (from the commandline) on the 1QOY.py? If that doesn't work you should install/download it again.
Groetnis,
Djurre
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12 years 5 months ago #826
by djurre
This error message often indicates you have an too old version of python. Update python and it should work.
Replied by djurre on topic Problem using martinize.py
Rajat Desikan wrote: AttributeError: 'tuple' object has no attribute 'count'
This error message often indicates you have an too old version of python. Update python and it should work.
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- Rajat Desikan
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12 years 5 months ago #830
by Rajat Desikan
Replied by Rajat Desikan on topic Problem using martinize.py
Thanks Djurre...I updated python and it worked...
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- Rajat Desikan
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12 years 5 months ago #832
by Rajat Desikan
Replied by Rajat Desikan on topic Problem using martinize.py
Hi
I have a protein consisting of 298 residues, but when I use martinize.py, only 294 residues are displayed. What is the problem? Is there a limit on the length of residues?
I have a protein consisting of 298 residues, but when I use martinize.py, only 294 residues are displayed. What is the problem? Is there a limit on the length of residues?
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- xavier
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12 years 3 months ago #878
by xavier
All residues should show up. Is the protein structure complete? May be missing residues? may be unknown residues?
Replied by xavier on topic Problem using martinize.py
Rajat Desikan wrote: Hi
I have a protein consisting of 298 residues, but when I use martinize.py, only 294 residues are displayed. What is the problem? Is there a limit on the length of residues?
All residues should show up. Is the protein structure complete? May be missing residues? may be unknown residues?
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