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Using insane.py to build protein/membrane complex
- zhiyue
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9 years 11 months ago #3791
by zhiyue
Shane
School of Pharmacy
University of Maryland
Baltimore, MD 21201, U.S.A.
Using insane.py to build protein/membrane complex was created by zhiyue
Hi all,
Seems that insane.py can be used to construct protein/membrane complex. If yes, I have several questions about how to achieve this.
1) What steps should I take sequentially to build the complex? I think the processes should be:
build CG structures for protein and single lipid ---> use insane.py to construct the complex. Correct me if I'm wrong.
2) I tried to use insane.py (the latest version downloaded from the website) like:
./insane.py -f prot_cg.pdb -p pope_cg.top -o prot_pope.gro -pbc rectangular -x 8 -y 8 -z 10 -d 1 -center -l POPE:256 -a 0.57 -sol W -charge
And I got the error message as
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Traceback (most recent call last):
File "./insane.py", line 559, in <module>
options[ar].setvalue([args.pop(0) for i in range(options[ar].num)])
IndexError: pop from empty list
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
I do not understand where this error originated and I am not sure whether I used the insane.py correctly.
Hope anyone can help me. Thanks in advance.
Best
Shane
Seems that insane.py can be used to construct protein/membrane complex. If yes, I have several questions about how to achieve this.
1) What steps should I take sequentially to build the complex? I think the processes should be:
build CG structures for protein and single lipid ---> use insane.py to construct the complex. Correct me if I'm wrong.
2) I tried to use insane.py (the latest version downloaded from the website) like:
./insane.py -f prot_cg.pdb -p pope_cg.top -o prot_pope.gro -pbc rectangular -x 8 -y 8 -z 10 -d 1 -center -l POPE:256 -a 0.57 -sol W -charge
And I got the error message as
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Traceback (most recent call last):
File "./insane.py", line 559, in <module>
options[ar].setvalue([args.pop(0) for i in range(options[ar].num)])
IndexError: pop from empty list
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
I do not understand where this error originated and I am not sure whether I used the insane.py correctly.
Hope anyone can help me. Thanks in advance.
Best
Shane
Shane
School of Pharmacy
University of Maryland
Baltimore, MD 21201, U.S.A.
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- tsjerk
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9 years 11 months ago #3792
by tsjerk
Replied by tsjerk on topic Using insane.py to build protein/membrane complex
You only need a protein as input, and insane will build a membrane around it, based on lipid templates defined in the program.
The -charge option requires an argument (the charge of the input file), which is not given and thus causes the exception to be raised. In addition, the number for lipids sets the relative abundance, not (yet) the desired number of lipids. So -l POPE:256 will give the same result as -l POPE. You here specify the box using -x/-y/-z, which overrules determining the box based on the dimensions of the protein and the distance between periodic images (-d).
The -charge option requires an argument (the charge of the input file), which is not given and thus causes the exception to be raised. In addition, the number for lipids sets the relative abundance, not (yet) the desired number of lipids. So -l POPE:256 will give the same result as -l POPE. You here specify the box using -x/-y/-z, which overrules determining the box based on the dimensions of the protein and the distance between periodic images (-d).
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- zhiyue
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9 years 11 months ago #3795
by zhiyue
Shane
School of Pharmacy
University of Maryland
Baltimore, MD 21201, U.S.A.
Replied by zhiyue on topic Using insane.py to build protein/membrane complex
Hi Tsjerk!
Thanks for your reply! It really helps!
I have another question. How can I use insane.py to build lipid bilayer around transmembrane domain of a protein if the protein has a large periplasmic domain? Thanks.
Best
Thanks for your reply! It really helps!
I have another question. How can I use insane.py to build lipid bilayer around transmembrane domain of a protein if the protein has a large periplasmic domain? Thanks.
Best
Shane
School of Pharmacy
University of Maryland
Baltimore, MD 21201, U.S.A.
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9 years 11 months ago #3796
by tsjerk
Replied by tsjerk on topic Using insane.py to build protein/membrane complex
I guess handling of such proteins needs to be optimized. There's now a hardcoded margin for deciding if atoms are in the membrane, which may cause atoms of the periplasmic domain to be listed as in the membrane. Do you have an example of such a protein? I can probably fix that the insane way, adding an option.
Cheers,
Cheers,
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9 years 11 months ago - 9 years 11 months ago #3797
by zhiyue
Shane
School of Pharmacy
University of Maryland
Baltimore, MD 21201, U.S.A.
Replied by zhiyue on topic Using insane.py to build protein/membrane complex
Hi Tsjerk,
Thanks for your reply. How can I send you the pdb file? Thanks.
Best
Thanks for your reply. How can I send you the pdb file? Thanks.
Best
Shane
School of Pharmacy
University of Maryland
Baltimore, MD 21201, U.S.A.
Last edit: 9 years 11 months ago by zhiyue. Reason: typo corrected
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