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normal Martinize2 protein with more than 99,999 atoms

  • TomasV
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1 year 2 weeks ago #9502 by TomasV
Martinize2 protein with more than 99,999 atoms was created by TomasV
Dear Martini users,

I am trying to martinize a protein complex with Martinize2, but I am getting the following error:
ValueError: invalid literal for int() with base 10: 'A0000'

I think this is because the complex is very large and so letters are used for atom numbers over 99,999 in the PDB file. I'm not sure how to go about fixing it or whether there is another approach I could use. Thanks!

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1 year 2 weeks ago #9503 by fgrunewald
Replied by fgrunewald on topic Martinize2 protein with more than 99,999 atoms
Try converting the PDB to a GRO and then give it to martinize2. Note that your resids, and chain identifiers might be messed up though due to the fixed field width in both formats.

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1 year 2 weeks ago #9504 by TomasV
Replied by TomasV on topic Martinize2 protein with more than 99,999 atoms
Thanks a lot for your suggestion! Martinize2 seems a lot happier now

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