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Insert multiple proteins with insane.py
- Vytautasrask
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8 years 11 months ago #4569
by Vytautasrask
Insert multiple proteins with insane.py was created by Vytautasrask
Is it possible to insert multiple proteins or multiple molecules of same protein with insane.py?
If it is possible then how?
If it is possible then how?
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- tsjerk
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8 years 11 months ago #4571
by tsjerk
Replied by tsjerk on topic Insert multiple proteins with insane.py
The easiest is to use DAFT, which is also a wrapper around insane for inserting multiple proteins. You can find it on
cgmartini.nl/cgmartini/index.php/tools2/proteins-and-bilayers
If you want to insert the proteins in a specific way, you can arrange the proteins without bilayer, and then pass them through INSANE for generating the membrane (and solvent). Just note that you need to add the option -ring to the command line to ensure that lipids are placed in between proteins. The option is called -ring, because it was added first to allow placement of lipids inside proteins arranged in a ring, but the principle is the same.
cgmartini.nl/cgmartini/index.php/tools2/proteins-and-bilayers
If you want to insert the proteins in a specific way, you can arrange the proteins without bilayer, and then pass them through INSANE for generating the membrane (and solvent). Just note that you need to add the option -ring to the command line to ensure that lipids are placed in between proteins. The option is called -ring, because it was added first to allow placement of lipids inside proteins arranged in a ring, but the principle is the same.
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- Jingjie Yeo
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8 years 10 months ago #4611
by Jingjie Yeo
Replied by Jingjie Yeo on topic Insert multiple proteins with insane.py
I am attempting to do the same, however there is an odd issue where the proteins are embedded in water instead of the membrane, and when I specified, -sol=PW, W water is inserted as well. May I know what the issue could be?
The command I issued was:
./daft.sh -cg A.pdb,A.top -cg B.pdb,B.top -cg C.pdb,C.top -cg E.pdb,E.top -d 3.5 -dz 5.0 -time 200 --insane{-l=DPPC,-l=CHOL,-l=GMO,-sol=PW}
The command I issued was:
./daft.sh -cg A.pdb,A.top -cg B.pdb,B.top -cg C.pdb,C.top -cg E.pdb,E.top -d 3.5 -dz 5.0 -time 200 --insane{-l=DPPC,-l=CHOL,-l=GMO,-sol=PW}
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- tsjerk
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8 years 10 months ago #4612
by tsjerk
Replied by tsjerk on topic Insert multiple proteins with insane.py
For DAFT I advise to place the proteins as they should be with respect to the bilayer center.
To set the solvent in DAFT, add it to the command line directly. The default is W. The solvent that you specify for insane is added, so the final insane command (echoed) will include -sol W -sol PW, giving a 1:1 mixture.
To set the solvent in DAFT, add it to the command line directly. The default is W. The solvent that you specify for insane is added, so the final insane command (echoed) will include -sol W -sol PW, giving a 1:1 mixture.
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