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insane to create a bilayer and nanodisc in the same box
- aa456
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1 year 9 months ago #9436
by aa456
insane to create a bilayer and nanodisc in the same box was created by aa456
I am using insane to create a nanodisc and then add another lipid bilayer into the box. The first command I use is:
insane -f 1D1_cg.pdb -o 1D1_cg-solvent.gro -p 1D1_cg-solvent.top -pbc cubic -x 15 -y 15 -z 15 -center -l POPC -disc ${r} -a 0.7 -ring -sol W -salt 0.15 -excl -1
This creates a solvated system with lipids filling my protein dimer.
Next, I have been running
insane -f 1D1_cg-solvent -o 1D1_added.gro -p 1D1_added.top -x 15 -y 15 -z 15 -dm 0.1 -l POPC -u POPC -a 0.7 -excl - 1
I am getting a filled upper leaflet but nothing in the lower leaflet. Increasing dm above .1 means I only get 25 lipids, and above 1, I get neither leaflet.
insane -f 1D1_cg.pdb -o 1D1_cg-solvent.gro -p 1D1_cg-solvent.top -pbc cubic -x 15 -y 15 -z 15 -center -l POPC -disc ${r} -a 0.7 -ring -sol W -salt 0.15 -excl -1
This creates a solvated system with lipids filling my protein dimer.
Next, I have been running
insane -f 1D1_cg-solvent -o 1D1_added.gro -p 1D1_added.top -x 15 -y 15 -z 15 -dm 0.1 -l POPC -u POPC -a 0.7 -excl - 1
I am getting a filled upper leaflet but nothing in the lower leaflet. Increasing dm above .1 means I only get 25 lipids, and above 1, I get neither leaflet.
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- tsjerk
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1 year 9 months ago #9447
by tsjerk
Replied by tsjerk on topic insane to create a bilayer and nanodisc in the same box
Hello,
Sorry for not answering earlier. Just happen to be the busiest weeks of the year, finishing up the teaching duties.
I think the problem is that the first pass adds the solvent, which overlaps with the membrane, so it gets excluded. Try to set up the disc with protein without solvent and then add the bilayer and the solvent in the second pass.
Hope it helps!
Sorry for not answering earlier. Just happen to be the busiest weeks of the year, finishing up the teaching duties.
I think the problem is that the first pass adds the solvent, which overlaps with the membrane, so it gets excluded. Try to set up the disc with protein without solvent and then add the bilayer and the solvent in the second pass.
Hope it helps!
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