Protein-RNA docking about lightdock HOT 22 CLOSED

Hi @aminijavad

Thanks for your message. This error originates from ProDy not selecting your RNA molecule for ANM calculations (flexibility). See line 42 in lightdock/structure/nm.py How do your ATOM records in your rna.pdb look like? My guess is that there is a mismatch between the way RNA bases are defined in your PDB and the way ProDy understands them. Also, please have a look at this tutorial: https://lightdock.org/tutorials/0.9.3/rna_docking#22-rna (if you haven't done so) since some preprocessing steps are needed for protein-RNA docking

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hi @aminijavad

Where did you send me the pdb file? I can't find it

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Oh sorry, I answered you from my email, not GitHub. Here you are

https://filebin.net/q4r1wy2whhb2q3o8

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Could you please send it uncompressed to [email protected]?

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sure

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Hi @aminijavad Sorry for the mistake as I wrongly read the error from your screenshot. The problem originates from your protein.pdb file instead. I verified your circ.pdb and there's no issue about it. Could you please share that pdb with me together with the exact command (lightdock3_setup.py) you are running? Attached screenshot of successful setup with your rna but with a different protein.

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Hi Jorge
Sure
I appreciate your help. I'll send it to your email. I ran these commands:

reduce -Trim A1_protein.pdb > 1A1T_A_noh.pdb
reduce -BUILD 1A1T_A_noh.pdb > 1A1T_A_h.pdb

pdb_reatom 1A1T_A_h.pdb > protein.pdb

lightdock3_setup.py protein.pdb rna.pdb -anm

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Thanks @aminijavad I have no issues doing the setup. See screenshot:

My guess is that your protein.pdb file is empty as pdb_reatom takes as an argument a number to renumber from:

pdb_reatom.py number pdb file

Could you please check?

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I'm wondering why your run performed without any error!
No, it wasn't.

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could you please share your commands?

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You can see them on the top of the screenshot:

lightdock3_setup.py A1_protein.pdb circ.pdb -anm

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Sorry to bother you, but is it possible to see your previous commands?

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There's nothing else. Just took the 2 pdb files you sent me and ran the setup

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I'm really confused, I still getting the error!

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I tried it and the setup works fine.

Try to update pyparsing since enablePackrat is a new method in version 3.0 and prody and lightdock don't specify the version of pyparsing in their requirements.

I hope this works @aminijavad

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Only to add to the discussion that pyparsing is not a LightDock dependency, but ProDy's.

@aminijavad if you try disabling RNA ligand flexibility with -anm -ar 10 -al 0 that would work and bypass the ProDy issue.

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We close this for now as the error could not be replicated in tow different settings

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I tried it and the setup works fine.

Try to update pyparsing since enablePackrat is a new method in version 3.0 and prody and lightdock don't specify the version of pyparsing in their requirements.

I hope this works @aminijavad

I will do it thank you

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We close this for now as the error could not be replicated in tow different settings

Thank you for your time Jorge

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Only to add to the discussion that pyparsing is not a LightDock dependency, but ProDy's.

@aminijavad if you try disabling RNA ligand flexibility with -anm -ar 10 -al 0 that would work and bypass the ProDy issue.

Sure, thank you

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