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Macromolecules separated in chains

PostPosted: Thu Aug 11, 2016 3:36 pm
by Tanjay
Hi,

I have a small problem when trying to run some dockings using PyRx, i have a pdbqt file which contains 4 chain and i can open this molecule using autodock 4 no problem but when i open the same file with PyRx, it gets separated into two macromolecules, one with chains B, C and D and the other with chain A. Because of this, i can't dock the whole molecule. Is there a way to make them one using PyRx or to make sure PyRx can recognize it as one molecule with 4 chains.

Btw, every chain was separated by a TER line in the pdbqt file, i tried removing them but it is still not working, using autodock 4, i added oxt but still PyRx keep seeing it as 2 differents molecules.

Thanks for your help,

Tanjay

Re: Macromolecules separated in chains

PostPosted: Sun Aug 14, 2016 12:33 pm
by sargis
Hi Tanjay,

Thanks for using PyRx. I can look into this. Do you know how I can get this file on my computer for testing?

Re: Macromolecules separated in chains

PostPosted: Tue Aug 16, 2016 4:00 pm
by Tanjay
I tried uploading it here but it says my file is too big unfortunately, if you could send me a private message with your email in it, i could send it to you no problem.

To be more precise, i'm using the AutoDock Wizard and when i click on Add Macromolecule(s) it gets added as two different molecules in the Molecules tab on the top left named myfile and myfile_a.

Thanks a lot for your help

Tanjay