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Is bbsc.sh script necessary for trasmembrane proteins?
- azadehalavi
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2 years 5 months ago - 2 years 5 months ago #9167
by azadehalavi
Is bbsc.sh script necessary for trasmembrane proteins? was created by azadehalavi
Dear all,
I would like to construct a martini model of a two trasmembrane domains (alpha helices) inside a lipid bilayer using martini 3 force field.
The itp file of one of the peptides is created using this command:
martinate.sh -f prot_A.pdb -martinize martinize2 -ffdir ../force_field -cg martini3001 --martinize-nt --martinize-cys=auto --martinize-p=backbone --martinize-dssp=mkdssp
Do I need to use the bbsc.sh script for the side-chain modifications?
I would appreciate your help.
Best regards,
Azadeh
I would like to construct a martini model of a two trasmembrane domains (alpha helices) inside a lipid bilayer using martini 3 force field.
The itp file of one of the peptides is created using this command:
martinate.sh -f prot_A.pdb -martinize martinize2 -ffdir ../force_field -cg martini3001 --martinize-nt --martinize-cys=auto --martinize-p=backbone --martinize-dssp=mkdssp
Do I need to use the bbsc.sh script for the side-chain modifications?
I would appreciate your help.
Best regards,
Azadeh
Last edit: 2 years 5 months ago by azadehalavi.
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- sebastian
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2 years 5 months ago #9177
by sebastian
Replied by sebastian on topic Is bbsc.sh script necessary for trasmembrane proteins?
Hi Azadeh,
Using martinize2, you can specify the -scfix option (or --martinize-scfix for martinate.sh) to add the side-chain corrections in the protein.itp.
Best,
Sebastian
Using martinize2, you can specify the -scfix option (or --martinize-scfix for martinate.sh) to add the side-chain corrections in the protein.itp.
Best,
Sebastian
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