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normal Martinize Script

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11 years 5 months ago #1255 by AlexC
Martinize Script was created by AlexC
I'm fairly new to MARTINI but i've had good results from the tutorials. Now I'm trying to use the martinize script on a PDB file I have created for the peptide A6R. However, I keep getting the following error/traceback:

martinize.py -f fg_A6R.pdb -o A6R.top -x A6R.pdb -dssp ./dssp -p backbone -v

...

Traceback (most recent call last):
File "martinize.py", line 4376, in <module>
main(options)
File "martinize.py", line 3975, in main
chains = [ Chain(options,) for chain in pdbChains(atoms) ]
File "martinize.py", line 3074, in __init__
self.breaks = self.type() in ("Protein") and breaks(self.residues) or []
File "martinize.py", line 2909, in breaks
return [ i+1 for i in range(len(bb)-1) if residueDistance2(bb,bb[i+1]) > cutoff]
File "martinize.py", line 2899, in residueDistance2
return min([distance2(i,j) for i in r1 for j in r2])
ValueError: min() arg is an empty sequence


I don't know if anyone can help with this, but any help would be greatly appreciated.

Alex

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11 years 5 months ago #1256 by xavier
Replied by xavier on topic Martinize Script
It is not clear either to me :)) But the script indicates some trouble with the chains ... you should try top clean up a bit your pdb file from unnecessary info, keep the part you are interested in, remove the hydrogens if any, there might be different chains, keep the one you want, try to martinize one chain at the time if necessary to identify the faulty one, ...

AlexC wrote: I'm fairly new to MARTINI but i've had good results from the tutorials. Now I'm trying to use the martinize script on a PDB file I have created for the peptide A6R. However, I keep getting the following error/traceback:

martinize.py -f fg_A6R.pdb -o A6R.top -x A6R.pdb -dssp ./dssp -p backbone -v

...

Traceback (most recent call last):
File "martinize.py", line 4376, in <module>
main(options)
File "martinize.py", line 3975, in main
chains = [ Chain(options,) for chain in pdbChains(atoms) ]
File "martinize.py", line 3074, in __init__
self.breaks = self.type() in ("Protein") and breaks(self.residues) or []
File "martinize.py", line 2909, in breaks
return [ i+1 for i in range(len(bb)-1) if residueDistance2(bb,bb[i+1]) > cutoff]
File "martinize.py", line 2899, in residueDistance2
return min([distance2(i,j) for i in r1 for j in r2])
ValueError: min() arg is an empty sequence


I don't know if anyone can help with this, but any help would be greatly appreciated.

Alex

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11 years 5 months ago #1282 by AlexC
Replied by AlexC on topic Martinize Script
Thanks for the help, we managed to generate our own files (which work perfectly) instead of using the martinize script, so unless we move onto larger peptides we should be fine.

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11 years 5 months ago #1285 by djurre
Replied by djurre on topic Martinize Script
I'm sorry it took a while to figure this out. What is probably going is that you have waters in your atomistic pdb with the same chain identifier as the protein/peptide. This messes up the distance measurement to check for chain breaks. In the next version of martinize that we will put online soon this will be fixed. In the mean time, you could change the chain identifier of the waters.

Thanks for letting us know!

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