1. Force Fields
  3. Lipids
  5. Problem with Cardiolipin

normal Problem with Cardiolipin

  • z.sichaib
  • z.sichaib's Avatar Topic Author
  • Offline
  • Senior Boarder
More
4 years 4 months ago #8369 by z.sichaib
Problem with Cardiolipin was created by z.sichaib
Dear Martini users/developers,

I am trying to use insane to build a membrane containing cardiolipin, among other lipids.
The CDL that I am getting looks wired. CDL should look like the one in Pic1 but I am obtaining something like the one in Pic2.

Link for the pictures: www.dropbox.com/sh/p1suz4z2wcvr8mq/AAA32...YGR0GsrvAU9yHKa?dl=0

This is the command line that I used to build the membrane:
python2.7 insane.py -f structure.gro -o structure_memb.gro -p topol.top -alname SDPE -alhead 'E P' -allink 'G G' -altail "DDDDD CCCC" -alname SDPS -alhead 'S P' -allink 'G G' -altail "DDDDD CCCC" -pbc cubic -box 14.1,14.1,16.8 -l POPC:40 -l SDPE:38.9 -l SDPS:14.2 -l SAPI:5.9 -l CDL2:0.8 -l CHOL:10 -u POPC:40 -u SDPE:38.9 -u SDPS:14.2 -u SAPI:5.9 -u CDL2:0.8 -u CHOL:10 -center -sol W

I tried both insane from www.cgmartini.nl/index.php/downloads/tools/239-insane
and the program downloaded with Pip2. With both, I am getting the same output.

Any help on this, please?

Best,

Zeineb

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

More
4 years 4 months ago #8378 by johnd
Replied by johnd on topic Problem with Cardiolipin
Hi Zeineb,

Not sure if you figured it out yet, but that's just the way that insane places the lipids on a grid when making a membrane. If you equilibrate the system for a bit, they will look like the one you have in pic2

John

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

  1. Force Fields
  3. Lipids
  5. Problem with Cardiolipin
Time to create page: 0.091 seconds