normal how to place protein at a certain distance away from the membrane

  • cm
  • cm's Avatar Topic Author
  • Offline
  • Senior Boarder
More
2 months 3 weeks ago #8210 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

Please Log in or Create an account to join the conversation.

  • cm
  • cm's Avatar Topic Author
  • Offline
  • Senior Boarder
More
2 months 2 weeks ago #8213 by cm
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

Please Log in or Create an account to join the conversation.

More
1 month 4 weeks ago #8233 by ms
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.

Please Log in or Create an account to join the conversation.

  • cm
  • cm's Avatar Topic Author
  • Offline
  • Senior Boarder
More
1 month 3 weeks ago - 1 month 3 weeks ago #8234 by cm
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.
Last edit: 1 month 3 weeks ago by cm.

Please Log in or Create an account to join the conversation.

More
1 month 2 weeks ago #8239 by riccardo
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 ?

Please Log in or Create an account to join the conversation.

Time to create page: 0.091 seconds