1. General topics
  3. Tools
  5. Can someone give me CG files for PDB ID: 6vsb

normal Can someone give me CG files for PDB ID: 6vsb

  • yogi@martini
  • yogi@martini's Avatar Topic Author
  • Offline
  • Junior Boarder
More
4 years 2 weeks ago - 1 year 10 months ago #8479 by yogi@martini
Can someone give me CG files for PDB ID: 6vsb was created by yogi@martini
Hello experts,

For the last few days, I am trying to create CG model for pdb (PDB ID: 6vsb), as many of you may know, it is pdb for spike protein of Coronavirus.

I tried martinize.py to get the CG model for it, but it's giving the missing residue error. Maybe some residues are missing in the structure. So I took another pdb for 6vsb from charmm server ( here ) and extracted protein coordinates. Now martinize.py is working but i think its messing up things. The generated topology and pdb files have mismatch of atom numbers.

Thanks.
Last edit: 1 year 10 months ago by yogi@martini. Reason: removed unnecessary details

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

More
4 years 1 week ago #8487 by vainikka
Replied by vainikka on topic Can someone give me CG files for PDB ID: 6vsb
Hi.

You could check out the predicted spike protein structure from I-TASSER website ( zhanglab.ccmb.med.umich.edu/C-I-TASSER/2019-nCov/ ).

I managed to run it through CHARMM-GUI, so it hopefully works with Martinize as well.

Good luck.

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

  1. General topics
  3. Tools
  5. Can someone give me CG files for PDB ID: 6vsb
Time to create page: 0.090 seconds