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Using insane.py
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9 years 11 months ago #3811
by tsjerk
Replied by tsjerk on topic Using insane.py
Insane only builds, and does so in the simplest conceivable manner. That's insane, but it works pretty well :) You can run the output through your preferred workflow, starting with energy minimization. The convergence of your system will go quite fast, especially if you have only one lipid component. For mixtures, you may need to equilibrate for up to microseconds. But there's no way around that, as no tool can build you a complex equilibrated membrane.
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9 years 11 months ago #3812
by Tocci_89
Replied by Tocci_89 on topic Using insane.py
Thank you for answer so readily!
Just another question: how can I include more than one protein into the bilayer? What would be the right command for insane in this case?
Just another question: how can I include more than one protein into the bilayer? What would be the right command for insane in this case?
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9 years 11 months ago #3813
by tsjerk
Replied by tsjerk on topic Using insane.py
You can arrange them the way you want to have them and then process them with insane adding the flag -ring. That was added for allowing placing lipids inside ring-like structures, but works for multiple proteins too.
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9 years 11 months ago #3814
by Tocci_89
Replied by Tocci_89 on topic Using insane.py
Perfect! Thank you for the tips!
I'll try this way, if any issue occurs I'll write back!
Best regards!
I'll try this way, if any issue occurs I'll write back!
Best regards!
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9 years 9 months ago #3951
by Sophia
Replied by Sophia on topic Using insane.py
Hi, I'm trying to use insane.py to set up a DOPC/CHOL bilayer in a 1:1 ratio. I copied the input further up this thread
./insane.py -l DOPC -l CHOL -a .5 -pbc rectangular -x 18 -y 18 -z 10 -o DOPC_CHOL_50%_martini.gro
but I get the following error
Traceback (most recent call last):
File "./insane.py", line 684, in <module>
pbcx = pbcy = pbcz = options["-d"].value + (options["-hole"] and options["-hole"].value or 0)
TypeError: unsupported operand type(s) for +: 'NoneType' and 'int'
I'm not sure why this isn't working anymore - can anyone help?
./insane.py -l DOPC -l CHOL -a .5 -pbc rectangular -x 18 -y 18 -z 10 -o DOPC_CHOL_50%_martini.gro
but I get the following error
Traceback (most recent call last):
File "./insane.py", line 684, in <module>
pbcx = pbcy = pbcz = options["-d"].value + (options["-hole"] and options["-hole"].value or 0)
TypeError: unsupported operand type(s) for +: 'NoneType' and 'int'
I'm not sure why this isn't working anymore - can anyone help?
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9 years 9 months ago #3952
by tsjerk
Replied by tsjerk on topic Using insane.py
That's odd. Thanks for reporting. I'll try to have it fixed ASAP.
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