- Posts: 31
Can someone give me CG files for PDB ID: 6vsb
- yogi@martini
- Topic Author
- Offline
- Junior Boarder
Less
More
4 years 3 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.
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.
- vainikka
- Offline
- Admin
Less
More
- Posts: 91
4 years 2 weeks 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.
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.
Time to create page: 0.092 seconds