normal Is bbsc.sh script necessary for trasmembrane proteins?

  • azadehalavi
  • azadehalavi's Avatar Topic Author
  • Offline
  • Fresh Boarder
More
2 years 5 months ago - 2 years 5 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: 2 years 5 months ago by azadehalavi.

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

More
2 years 5 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

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

Time to create page: 0.121 seconds