normal Creating CG model for Cytochrom C

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12 years 2 months ago #903 by dariush
Creating CG model for Cytochrom C was created by dariush
I am going to make CG model for Cytochrom C protein according the
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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12 years 2 months ago #904 by dariush
Replied by dariush on topic Creating CG model for Cytochrom C
I have changed my .ssd file (it had something wrong in it). Now I have this error:

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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12 years 2 months ago #905 by djurre
Replied by djurre on topic Creating CG model for Cytochrom C
Are you sure you want to specify a *.ssd file yourself, instead of letting martinize create it for you? (Use: -dssp /PATH/TO/DSSP/EXECUTABLE)

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12 years 2 months ago #906 by dariush
Replied by dariush on topic Creating CG model for Cytochrom C
I did not create myself; also I could not make it by
(-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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12 years 2 months ago #907 by djurre
Replied by djurre on topic Creating CG model for Cytochrom C
A few thinks might go wrong: cytochrome C is deposited as an dimer. If you haven't removed half, the *.ssd file will be wrong. That said, for this works perfect:

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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12 years 2 months ago #911 by dariush
Replied by dariush on topic Creating CG model for Cytochrom C
Thank you. I follow that command. I also did several changes, and removed extra lines in PDB file. I got below error. It shows some progress :)


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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12 years 2 months ago #912 by djurre
Replied by djurre on topic Creating CG model for Cytochrom C
What version of Python do you use? (type 'python --version' on the commandline and it will tell you.) The martinize script only works with recent versions of python (eg. 2.6, 2.7).

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12 years 2 months ago #914 by dariush
Replied by dariush on topic Creating CG model for Cytochrom C
At first, thanks for your help.
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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12 years 2 months ago #915 by dariush
Replied by dariush on topic Creating CG model for Cytochrom C
My work stucked up. If anybody knows how can I model HEME in cythochrome C, it is appreciated.
Thanks,
Dariush

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11 years 10 months ago #943 by xavier
Replied by xavier on topic Creating CG model for Cytochrom C

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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11 years 10 months ago #944 by dariush
Replied by dariush on topic Creating CG model for Cytochrom C
No, we could not make model for HEME. If you could do it please share that with us.
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11 years 10 months ago #950 by xavier
Replied by xavier on topic Creating CG model for Cytochrom C
Unfortunately the models are still in development, meaning they are not accurate and ready to use.

dariush wrote: No, we could not make model for HEME. If you could do it please share that with us.
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11 years 7 months ago #1062 by vamsi9k
Replied by vamsi9k on topic Creating CG model for Cytochrom C
Hi,

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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11 years 7 months ago #1063 by dariush
Replied by dariush on topic Creating CG model for Cytochrom C
I have no idea... :(

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11 years 7 months ago #1065 by djurre

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