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normal Martinize .pdb output missing beads

  • Jingjie Yeo
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8 years 11 months 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

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8 years 11 months 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.

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  1. Force Fields
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  5. Martinize .pdb output missing beads
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