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how to place protein at a certain distance away from the membrane
- cm
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4 years 8 months ago #8210
by cm
how to place protein at a certain distance away from the membrane was created by cm
hi,
i am following this tutorial
cgmartini.nl/index.php/tutorials-general-introduction/proteins .
now using this command "insane.py -f kalp.gro -o system.gro -p system.top -pbc square -box 10,10,10 -l DPPC -center -sol W"
the protein will be centered into the membrane.
But my question is how i can place the protein 10 angstrom away from the membrane but not in membrane because "-center" will place the protein in the center of membrane.
Also can anyone please suggest me how i can change the lipid ratio because i want to make a bi-layer containing 50%popc and 50% popg.
thanking you
i am following this tutorial
cgmartini.nl/index.php/tutorials-general-introduction/proteins .
now using this command "insane.py -f kalp.gro -o system.gro -p system.top -pbc square -box 10,10,10 -l DPPC -center -sol W"
the protein will be centered into the membrane.
But my question is how i can place the protein 10 angstrom away from the membrane but not in membrane because "-center" will place the protein in the center of membrane.
Also can anyone please suggest me how i can change the lipid ratio because i want to make a bi-layer containing 50%popc and 50% popg.
thanking you
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- cm
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4 years 7 months ago #8213
by cm
Replied by cm on topic how to place protein at a certain distance away from the membrane
i am using this command
insane.py -f *.gro -o *.gro -p system.top -pbc square -box 20,20,20 -l POPC:0.1 l POPG:0.1 -center 0 0 30 -sol W
but the error is coming is
Traceback (most recent call last):
File "./insane.py" , line 559 in <module>
options[ar].setvalue([arg.pop(0) for i in range/(options[ar].num)])
keyerror:'0'
Can anyone please help me in this regards
thanking you
insane.py -f *.gro -o *.gro -p system.top -pbc square -box 20,20,20 -l POPC:0.1 l POPG:0.1 -center 0 0 30 -sol W
but the error is coming is
Traceback (most recent call last):
File "./insane.py" , line 559 in <module>
options[ar].setvalue([arg.pop(0) for i in range/(options[ar].num)])
keyerror:'0'
Can anyone please help me in this regards
thanking you
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- ms
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4 years 7 months ago #8233
by ms
Replied by ms on topic how to place protein at a certain distance away from the membrane
Hi cm,
I am rather new to the usage of insane, but i hope my answer can help you.
The center flag do not take any argument. That's what the error is saying.
In your case, you should use a different flag, -dm. The argument of this flag should be 10 or -10 depending on which side you want to send the protein.
Also, if you want 50% of each of your lipids, you should give 5 as argument.
Thus, your command would be:
insane.py -f *.gro -o *.gro -p system.top -pbc square -box 20,20,20 -l POPC:5 -l POPG:5 -center -dm 10 -sol W
I hope this settle your issue.
Regards.
I am rather new to the usage of insane, but i hope my answer can help you.
The center flag do not take any argument. That's what the error is saying.
In your case, you should use a different flag, -dm. The argument of this flag should be 10 or -10 depending on which side you want to send the protein.
Also, if you want 50% of each of your lipids, you should give 5 as argument.
Thus, your command would be:
insane.py -f *.gro -o *.gro -p system.top -pbc square -box 20,20,20 -l POPC:5 -l POPG:5 -center -dm 10 -sol W
I hope this settle your issue.
Regards.
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- cm
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4 years 7 months ago - 4 years 7 months ago #8234
by cm
Replied by cm on topic how to place protein at a certain distance away from the membrane
thank you so much for your reply. i have already solve that problem by using -dm option.When i am using non polarizable water system the minimization and equilibration is going smoothly. But when i am incorporating polarizable water in to that above command , the following error is coming
"invalid order for directive molecule type"
do you have any idea...why this is happening.
Can anyone please suggest me...what water model should i take ..my system contain mixture of lipid and protein.
"invalid order for directive molecule type"
do you have any idea...why this is happening.
Can anyone please suggest me...what water model should i take ..my system contain mixture of lipid and protein.
Last edit: 4 years 7 months ago by cm.
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- riccardo
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4 years 6 months ago #8239
by riccardo
Replied by riccardo on topic how to place protein at a certain distance away from the membrane
Hi, regarding the error "invalid order for directive molecule type": it sounds like something is going wrong with the way you are #including itp files in the top file? Did you have a careful look at the example files accessible via this page
www.cgmartini.nl/index.php/120-polarize
?
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