unanswered Backward mapping fails with index out of range error

  • khZhang
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11 months 3 weeks ago #9656 by khZhang
Dear Martini Users,

I am trying to convert a CG system back to full atom resolution. Upon running ./initram (version downloaded from github.com/tsjerk/backward ), mapping files for Martini 3 obtained from bottom of this tutorial.

The command I used is:
./initram.sh -f cg-chainA.pdb -o output-chainA.pdb -p topol.top -from martini -to charmm36

And I see the following error:
GROMACS VERSION:
MPI: false
/Users/doriszhang/Desktop/backward-test/backward.py -f cg-chainA.pdb -raw projected.gro -o 0-backward.gro -kick 0.05 -sol -p topol.top -po backmapped.top -n backmapped.ndx -from martini -to charmm36 -solname SOL
Traceback (most recent call last):
  File "/Users/doriszhang/Desktop/backward-test/backward.py", line 760, in <module>
    struc = Structure(options["-f"].value,strict=options["-strict"].value)
  File "/Users/doriszhang/Desktop/backward-test/backward.py", line 519, in __init__
    d12.append(d12[-1])
IndexError: list index out of range

I've looked through the forum for similar errors and tried the suggested fixes (checking mapping files and make sure that they list the same atoms as topology file, trying to backmap a single chain first, backmapping a single residue). But regardless of the changes I make to the mapping files (I did edit 3 mapping files, hope I didn't break anything. The mapping files were for ASP, GLU, and HIS), I would still get the same error about index out of range at that same line. And I cannot backmap either a single chain or residue.

Does anyone have any idea what could be happening here? I can provide the input files in a link. Any help is greatly appreciated!

Thank you in advance,
Doris

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