unanswered Truncated heavy chains on antibody using martinize.py

  • amjadkchy
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9 months 3 weeks ago #9672 by amjadkchy

I am trying to build a CG model of an antibody using martinize.py (version 2.6.3, python3). My command is:

python martinize.py -f nistmab.pdb -o single-mab.top -x nistmab-CG.pdb -ss nistmab.dssp -ff martini22

nistmab.dssp is the dssp file generated using mkdssp version 4.4.

This runs, and it does seem to detect that two of the chains have 440 residues, but when I open the nistmab-CG.pdb file all four chains only have 214 residues in them.

If I do not feed martinize.py any secondary structure information, then the resulting nistmab-CG.pdb file does have chains of the correct length.

Has anybody else encountered this problem, and any suggestions on how to troubleshoot is greatly appreciated.

Thank you!

INFO MARTINIZE, script version 2.6_3
INFO If you use this script please cite:
INFO de Jong et al., J. Chem. Theory Comput., 2013, DOI:10.1021/ct300646g
INFO Chain termini will be charged
INFO Residues at chain brakes will not be charged
INFO The martini22 forcefield will be used.
INFO Local elastic bonds will be used for extended regions.
INFO Read input structure from file.
INFO Input structure is a PDB file.
INFO Found 4 chains:
INFO 1: A (), 3243 atoms in 214 residues.
INFO 2: B (), 6739 atoms in 440 residues.
INFO 3: C (), 3243 atoms in 214 residues.
INFO 4: D (), 6737 atoms in 440 residues.
INFO Total size of the system: 1308 residues.
INFO Will read secondary structure from file (assuming DSSP output).
INFO Writing coarse grained structure.
INFO (Average) Secondary structure has been determined (see head of .itp-file).
INFO Created coarsegrained topology
INFO Created coarsegrained topology
INFO Created coarsegrained topology
INFO Created coarsegrained topology
INFO Written 4 ITP files
INFO Output contains 4 molecules:
INFO 1-> Protein_A (chain A)
INFO 2-> Protein_B (chain B)
INFO 3-> Protein_C (chain C)
INFO 4-> Protein_D (chain D)
INFO Written topology files
INFO Note: Cysteine bonds are 0.24 nm constraints, instead of the published 0.39nm/5000kJ/mol.

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