normal Is bbsc.sh script necessary for trasmembrane proteins?

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1 year 4 months ago - 1 year 3 months ago #9167 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
Last edit: 1 year 3 months ago by azadehalavi.

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1 year 3 months ago #9177 by sebastian
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

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