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Error during tutorial about converting AA to CG?
- xudongh
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11 years 5 months ago - 11 years 5 months ago #1195
by xudongh
Error during tutorial about converting AA to CG? was created by xudongh
Hello, I am following the tutorial about converting AA to CG , and this is the command I get
*Note( I installed DSSP, atleast I think i installed it correctly. When I do /usr/local/bin and check, dsspcmbi is in fact there in the directory )
xus-macbook-pro:proteins xudongh$ ./martinize.py -f 1UBQ.pdb -o system.top -x cg_1UBQ.pdb -dssp /usr/local/bin/dsspcmbi -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 2 chains:
INFO 1: A (Protein), 602 atoms in 76 residues.
INFO 2: A (Water), 58 atoms in 58 residues.
INFO Removing 58 water molecules (chain A).
INFO Merges:
INFO Total size of the system: 76 residues.
sh: /usr/local/bin/dsspcmbi: cannot execute binary file
Traceback (most recent call last):
File "./martinize.py", line 2152, in <module>
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 "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py", line 679, in __init__
errread, errwrite)
File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py", line 1228, in _execute_child
raise child_exception
OSError: [Errno 8] Exec format error
**Actually I know I have DSSP installed, because when I do do_dssp in command window, gromacs shows up in command window, so I don't know why I'm getting errors for the stuff I'm trying to do above.
Thanks :)
*Note( I installed DSSP, atleast I think i installed it correctly. When I do /usr/local/bin and check, dsspcmbi is in fact there in the directory )
xus-macbook-pro:proteins xudongh$ ./martinize.py -f 1UBQ.pdb -o system.top -x cg_1UBQ.pdb -dssp /usr/local/bin/dsspcmbi -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 2 chains:
INFO 1: A (Protein), 602 atoms in 76 residues.
INFO 2: A (Water), 58 atoms in 58 residues.
INFO Removing 58 water molecules (chain A).
INFO Merges:
INFO Total size of the system: 76 residues.
sh: /usr/local/bin/dsspcmbi: cannot execute binary file
Traceback (most recent call last):
File "./martinize.py", line 2152, in <module>
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 "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py", line 679, in __init__
errread, errwrite)
File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py", line 1228, in _execute_child
raise child_exception
OSError: [Errno 8] Exec format error
**Actually I know I have DSSP installed, because when I do do_dssp in command window, gromacs shows up in command window, so I don't know why I'm getting errors for the stuff I'm trying to do above.
Thanks :)
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- djurre
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11 years 5 months ago #1197
by djurre
Replied by djurre on topic Error during tutorial about converting AA to CG?
Thanks for letting us know. I can't see what the problem is, but a collegue reported a similar recently. I'll look in to it. In the mean time, a work around is to create a secondary structure file with do_dssp and give that to martinize.py using the -ss option.
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- tsjerk
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11 years 5 months ago #1200
by tsjerk
Replied by tsjerk on topic Error during tutorial about converting AA to CG?
Hi,
I haven't encountered this error before. It appears that there is a problem calling DSSP from within martinize. Is the program executable, and can you run it manually as
/usr/local/bin/dsspcmbi -i /dev/stdin -o test.ssd < 1UBQ.pdb
Cheers,
Tsjerk
I haven't encountered this error before. It appears that there is a problem calling DSSP from within martinize. Is the program executable, and can you run it manually as
/usr/local/bin/dsspcmbi -i /dev/stdin -o test.ssd < 1UBQ.pdb
Cheers,
Tsjerk
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- xudongh
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11 years 5 months ago #1202
by xudongh
I'm sorry I'm not very familiar with do_dssp command, how exactly should the input be? do_dssp 1UBQ.pdb?
Thanks
Replied by xudongh on topic Error during tutorial about converting AA to CG?
djurre wrote: Thanks for letting us know. I can't see what the problem is, but a collegue reported a similar recently. I'll look in to it. In the mean time, a work around is to create a secondary structure file with do_dssp and give that to martinize.py using the -ss option.
I'm sorry I'm not very familiar with do_dssp command, how exactly should the input be? do_dssp 1UBQ.pdb?
Thanks
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- xudongh
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11 years 5 months ago #1203
by xudongh
Replied by xudongh on topic Error during tutorial about converting AA to CG?
Hi,
This is the error I get when I try to run the command you suggested:
xus-macbook-pro:proteins xudongh$ /usr/local/bin/dsspcmbi -i /dev/stdin -o test.ssd < 1UBQ.pdb
-bash: /usr/local/bin/dsspcmbi: cannot execute binary file
I think it's because I have a mac, not a linux, therefore this binary file cannot be executed in the way we normally do. However, do_dssp still works it seems.
This is the error I get when I try to run the command you suggested:
xus-macbook-pro:proteins xudongh$ /usr/local/bin/dsspcmbi -i /dev/stdin -o test.ssd < 1UBQ.pdb
-bash: /usr/local/bin/dsspcmbi: cannot execute binary file
I think it's because I have a mac, not a linux, therefore this binary file cannot be executed in the way we normally do. However, do_dssp still works it seems.
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- tsjerk
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11 years 5 months ago #1204
by tsjerk
Replied by tsjerk on topic Error during tutorial about converting AA to CG?
Hi Xudong,
So it's the same error that martinize gives, showing that the cause lies outside of that script. Have you assured that the dssp binary is executable?:
ls -l /usr/local/bin/dsspcmbi
Does the output file generated by do_dssp make sense, and does it work as explicit input to martinize? It would be odd, as do_dssp makes a similar system call, but maybe there's a subtle difference in the call. In that case, I'll have to dive into the do_dssp source code...
Cheers,
Tsjerk
So it's the same error that martinize gives, showing that the cause lies outside of that script. Have you assured that the dssp binary is executable?:
ls -l /usr/local/bin/dsspcmbi
Does the output file generated by do_dssp make sense, and does it work as explicit input to martinize? It would be odd, as do_dssp makes a similar system call, but maybe there's a subtle difference in the call. In that case, I'll have to dive into the do_dssp source code...
Cheers,
Tsjerk
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- xudongh
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11 years 5 months ago #1205
by xudongh
Replied by xudongh on topic Error during tutorial about converting AA to CG?
This is the output it gave me based on your command:
xus-macbook-pro:proteins xudongh$ ls -l /usr/local/bin/dsspcmbi
lrwxr-xr-x 1 root wheel 20 Oct 28 14:32 /usr/local/bin/dsspcmbi -> ../src/dssp/dsspcmbi
I haven't done the do_dssp way yet, I do not know how to do it. Becuase i dont know what input parameter is required. By reading do_dssp -h, it seems that it requires files I do not currently have. such as xtc files
xus-macbook-pro:proteins xudongh$ ls -l /usr/local/bin/dsspcmbi
lrwxr-xr-x 1 root wheel 20 Oct 28 14:32 /usr/local/bin/dsspcmbi -> ../src/dssp/dsspcmbi
I haven't done the do_dssp way yet, I do not know how to do it. Becuase i dont know what input parameter is required. By reading do_dssp -h, it seems that it requires files I do not currently have. such as xtc files
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- xudongh
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11 years 5 months ago #1206
by xudongh
Actually I have another question, if I start using this on a linux, the part where it says : ./martinize.py -f 1UBQ.pdb -o system.top -x cg_1UBQ.pdb -dssp /wherever/dsspcmbi -p backbone
***What do I put in the /wherever/ part?
Thanks
Replied by xudongh on topic Error during tutorial about converting AA to CG?
xudongh wrote: Hi,
This is the error I get when I try to run the command you suggested:
xus-macbook-pro:proteins xudongh$ /usr/local/bin/dsspcmbi -i /dev/stdin -o test.ssd < 1UBQ.pdb
-bash: /usr/local/bin/dsspcmbi: cannot execute binary file
I think it's because I have a mac, not a linux, therefore this binary file cannot be executed in the way we normally do. However, do_dssp still works it seems.
Actually I have another question, if I start using this on a linux, the part where it says : ./martinize.py -f 1UBQ.pdb -o system.top -x cg_1UBQ.pdb -dssp /wherever/dsspcmbi -p backbone
***What do I put in the /wherever/ part?
Thanks
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- tsjerk
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11 years 5 months ago #1207
by tsjerk
Replied by tsjerk on topic Error during tutorial about converting AA to CG?
It should be the path to dsspcmbi binary, similar to the case on a Mac. If you downloaded it yourself, it is most likely somewhere in your home directory.
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- xudongh
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11 years 5 months ago #1208
by xudongh
Replied by xudongh on topic Error during tutorial about converting AA to CG?
Is.there a way to make that binary call universal? So we.don't.have to type the.path to it?
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- tsjerk
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11 years 5 months ago #1209
by tsjerk
Replied by tsjerk on topic Error during tutorial about converting AA to CG?
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