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porekhov / palmitoylize

a script for palmitoylation of coarse-grained MARTINI protein models
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IndexError: list index out of range #1

Open skaswur opened 2 years ago

skaswur commented 2 years ago

Hello porekhov,

I have used palmitoylize.py successfully for some proteins but recently I am getting some strange index error. I have a CG protein structure in which CYS is position on number two.

ATOM 3 BB CYS 2 54.273 38.499 81.017 1.00 0.02 PROA ATOM 4 SC1 CYS 2 57.047 38.000 81.355 1.00 0.02 PROA

However, when running the command python3 palmitoylize.py -p palm_cg.pdb -i PROA_P.itp -d 1 -c 2 I get the error below:

% python3 palmitoylize.py -p palm_cg.pdb -i PROA_P.itp -d 1 -c 2 Traceback (most recent call last): File "/Users/palmitoylize/palmitoylize.py", line 129, in if cur_section == 'at' and fields[3] == 'CYS' and fields[4] == 'SC1' and fields[2] in cys2cyp: IndexError: list index out of range

porekhov commented 2 years ago

Hi skaswur,

it looks like the corresponding line in the itp file is not complete. Can you please share the input itp/pdb files either in this thread or by sending to orekhov@mail.bio.msu.ru?