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Protein error
- vamsi9k
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11 years 8 months ago #1061
by vamsi9k
Protein error was created by vamsi9k
Hi all,
I would like to run martini for protein in water but while creating topology file , getting following error
This protein is having two chains , please explain me where i am going wrong (all example runs were successful)
This is my command like
python martinize.py -f 1unl.pdb -o 1unl.top -x 1unl.gro -v -dssp ./dssp (dssp in current directory)
I am using python 2.7
Thank you in advance
Traceback (most recent call last):
File "./martinize.py", line 4375, in <module>
main(options)
File "./martinize.py", line 4259, in main
top = Topology(mol[0],options=options,name=name)
File "./martinize.py", line 3537, in __init__
self.fromAminoAcidSequence(other)
File "./martinize.py", line 3760, in fromAminoAcidSequence
positionCa = [residue[1][4:] for residue in chain.residues]
File "./martinize.py", line 2871, in __getitem__
return list.__getitem__(self,tag)
IndexError: list index out of range
I would like to run martini for protein in water but while creating topology file , getting following error
This protein is having two chains , please explain me where i am going wrong (all example runs were successful)
This is my command like
python martinize.py -f 1unl.pdb -o 1unl.top -x 1unl.gro -v -dssp ./dssp (dssp in current directory)
I am using python 2.7
Thank you in advance
Traceback (most recent call last):
File "./martinize.py", line 4375, in <module>
main(options)
File "./martinize.py", line 4259, in main
top = Topology(mol[0],options=options,name=name)
File "./martinize.py", line 3537, in __init__
self.fromAminoAcidSequence(other)
File "./martinize.py", line 3760, in fromAminoAcidSequence
positionCa = [residue[1][4:] for residue in chain.residues]
File "./martinize.py", line 2871, in __getitem__
return list.__getitem__(self,tag)
IndexError: list index out of range
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- djurre
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11 years 8 months ago #1064
by djurre
Replied by djurre on topic Protein error
The problem is in chains D&E. The last residue is a GLY, but it actually only consist of a single nitrogen. The program chokes at that. I'm not sure if that occurs a lot, in that case we should have the program fixed. For now, your best shot is just remove the last residue from chain D&E in your pdb.
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- vamsi9k
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11 years 8 months ago #1066
by vamsi9k
Replied by vamsi9k on topic Protein error
Thank you so much ... it worked
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11 years 8 months ago #1067
by vamsi9k
Replied by vamsi9k on topic Protein error
Thank you very much for your quick reply.. I would like to ask another question
I would like to study protein-protein interactions using martini coarse grain . how do i calculate rmsd , rmsf and PCA from coarse grain trajectories, as i could not see any ca atoms listing or back bone listing while running g_rms tool.
Is PCA of CG is directly comparable that of atomic scale simulations?
This information help me a lot for my research project ...
Thank you so much
I would like to study protein-protein interactions using martini coarse grain . how do i calculate rmsd , rmsf and PCA from coarse grain trajectories, as i could not see any ca atoms listing or back bone listing while running g_rms tool.
Is PCA of CG is directly comparable that of atomic scale simulations?
This information help me a lot for my research project ...
Thank you so much
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11 years 8 months ago #1068
by djurre
Replied by djurre on topic Protein error
Next time, it would be better to start a new thread for a new question.
In stead of Ca positions you could use the BB-bead positions. They are at the center of mass of all BB-beads, so any results will not be exactly the same as the atomistic analysis.
In stead of Ca positions you could use the BB-bead positions. They are at the center of mass of all BB-beads, so any results will not be exactly the same as the atomistic analysis.
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