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Relax with multiple small molecules

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Relax with multiple small molecules

Fast relax works fine with two ligands when the .params file are provided in the format.

-extra_res_fa LG1.params LG2.params

But when the same protocol is used with a few added flags such as

-packing:resfile resfile

it fails with the following message

[ ERROR ] UtilityExitException
ERROR: In protocols::jd2::JobsContainer [] operator: index is out of range (less than 1 or greater than total jobs).

Any suggestion how to fix this.

Thank you in advance.

Post Situation: 
Sun, 2019-05-26 19:34

I can't really see why that would be related to the number of params files given.

Instead, I think it might be due to Rosetta not getting the correct number of jobs/input structures for some reason, potentially a bad command line.

One thing to do is to double check your input command and options file, to see if there's some issue with them. (Are you putting everything in the correct location.) In particular, I'd see if there's any spurious non-printable characters in the options file or command line (Two common ones is having a DOS/Windows line endings for an option file, or having an em-dash or en-dash instead of a ASCII hyphen for the dashes in the options.)

Failing that, could you post (copy/paste) your command line and options files as-used?


Mon, 2019-06-24 15:19