"ReadMOLFile-Error: bad atom count" error when open exported .sdf file in PyMOL

forlilab / Meeko

Interfacing RDKit and AutoDock

GNU Lesser General Public License v2.1

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"ReadMOLFile-Error: bad atom count" error when open exported .sdf file in PyMOL #68

Closed Le-Phung-Hien closed 10 months ago

Le-Phung-Hien commented 10 months ago

Hi,

I have converted a vina results file to .sdf file using Meeko 0.5.0. capsaicin_out.pdbqt.txt capsaicin_out.sdf.txt

When open the sdf file in PyMOL 2.5.5, I have a "ReadMOLFile-Error: bad atom count" error. It happen with every file exported by Meeko. At first glance, the molecules can still be displayed and processed as normal in PyMOL.

I just wonder what can cause this error?

Thanks!

rwxayheee commented 10 months ago

Hi @Le-Phung-Hien Could you try removing the newlines at the end of sdf file? That fixed the "ReadMOLFile-Error: bad atom count" for me

diogomart commented 10 months ago

Fixed in aeffc06ff90771f62c4d169566a2743ea6c3b34f Thank you @Le-Phung-Hien for reporting and @rwxayheee for finding the problem!

Le-Phung-Hien commented 10 months ago

@rwxayheee @diogomart Thanks a lot!