- Posts: 10
Martinize .pdb output missing beads
- Jingjie Yeo
- Topic Author
- Offline
- Fresh Boarder
Less
More
9 years 5 days ago #4531
by Jingjie Yeo
Martinize .pdb output missing beads was created by Jingjie Yeo
I am having some trouble with the martinize script. I am trying to coarse-grain a pdb file which I generated using gromacs. The output pdb is giving me a different number of beads as compared to the .itp files. I have two chains within this pdb file, it seems like the C-termini residue is missing for both chains within the pdb but not the .itp files. May I know whether there is some special consideration for PDBs with 2 chains of proteins?
The command that I used was:
martinize.py -f in.pdb -o out.top -x out.pdb -dssp /usr/bin/mkdssp -p Backbone -ff martini21
The command that I used was:
martinize.py -f in.pdb -o out.top -x out.pdb -dssp /usr/bin/mkdssp -p Backbone -ff martini21
Please Log in or Create an account to join the conversation.
- Jingjie Yeo
- Topic Author
- Offline
- Fresh Boarder
Less
More
- Posts: 10
9 years 5 days ago #4532
by Jingjie Yeo
Replied by Jingjie Yeo on topic Martinize .pdb output missing beads
I realized what the error was, I mislabelled the terminal oxygen in the pdb.
Please Log in or Create an account to join the conversation.
Time to create page: 0.088 seconds