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Creating CG model for Cytochrom C
- dariush
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information on MARTINI website, but I could not do it.
I have PDB file of this protein and I have made .ssd file.
I could not get a master topology file (.top), and a protein topology
file (.itp), but I got coarse grain structure (.pdb). However, I think .pdb file alos was not created correctly.
The error is:
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'
Could you please help me out?
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- dariush
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Traceback (most recent call last):
File "./martinize.py", line 2127, in <module>
if ssfile[0].isdigit():
IndexError: list index out of range
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- djurre
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- dariush
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(-dssp /PATH/TO/DSSP/EXECUTABLE).
I have made it by dssp to ssd script and it contains:
104
~~HHHHHHHHHHHTTTT~~~STT~~~~SS~~~TT~TTSBTT~~TT~~~~HHHHH~~~B~SHHHHHHHTT~HHHHSTT~S~~~~~~~SHHHHHHHHHHHHHHHH~
I think it is correct.
Thanks,
Dariush
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- djurre
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martinize.py -f 3cyt.pdb -v -dssp /home/joe/dsspcmbi -o 3cyt.top -x CG.pdb
where instead of /home/joe/dsspcmbi you of course have to fill in the location of your dssp binary.
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- dariush
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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.
DEBUG Splitting chain A in 2 chains
INFO Found 2 chains:
INFO 1: A (Protein), 823 atoms in 104 residues.
INFO 2: A (Unknown), 43 atoms in 1 residues.
INFO Removing HETATM chain A consisting of 1 residues.
INFO Merges:
INFO Total size of the system: 104 residues.
DEBUG Old version of DSSP; Executing '/data/users/darmo/dssp/dsspcmbi -- chain_A.ssd'
DEBUG DSSP determined secondary structure:
HHHHHHHHHHHTTTT STT SS TT TTSBTT TT HHHHH B SHHHHHHHTT HHHHSTT S SHHHHHHHHHHHHHHHH
INFO Writing coarse grained structure.
INFO (Average) Secondary structure has been determined (see head of .itp-file).
DEBUG CC1111HHH2222TTTTCCCSTTCCCCSSCCCTTCTTSCTTCCTTCCCC13332CCCCCS1113222TTC3333STTCSCCCCCCCS1111HHHHHHHH2222C
DEBUG
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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- dariush
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Afterward, everything went well and I could get .pdb and .itp and .top files. Also using editconf I could create conf.gro file.
However, there was not HEM and HOH groups in the both .pdb and .gro files (you know Cytochrome C has HEME and it is very important part of this molecule). Could you please let me know how can I add them to these files?
Thanks,
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- dariush
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Thanks,
Dariush
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- xavier
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dariush wrote: My work stucked up. If anybody knows how can I model HEME in cythochrome C, it is appreciated.
Thanks,
Dariush
Sorry for the delay in answering a problem with the server made us unaware of the presence of new messages.
Did you finally fix your problem?
Note that we are working on getting a parameters for HEME and CHLOROPHIL molecules but nothing quite finished yet.
I hope this helps.
XAvier.
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- dariush
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- xavier
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dariush wrote: No, we could not make model for HEME. If you could do it please share that with us.
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- vamsi9k
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i am facing same problem as you had, but not able able to resolve it .. please explain me where exactly problem is and i am using python version 2.6 .
I am not very sure if it is problem with my pdb (1unl_A_D).
Thank you in advance for your help
errot :
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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- dariush
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