Unable to split the ligand SDF file successfully

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1

GROMACS version: 2021
GROMACS modification: Yes/No
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Error in splitting the ligands SDF file (animalia)
Error in splitting the ligands SDF file (animalia)1920×999 89 KB

Hi and good day everyone. For your information, I want to split the “ligand SDF file” (CMNPD-export.sdf is the filename downloaded in my working directory) that contains a total of 413 ligands by using the command “obabel -isdf CMNPD-export.sdf -osdf -O *.sdf - -split” after I have downloaded the ligand SDF file from the Comprehensive Marine Natural Product Database (CMNPD) for molecular docking and molecular dynamic simulation research. However, an error pops up as shown below:

Open Babel Error in TetStereoToWedgeHash
Failed to set stereochemistry as unable to find an available bond

Hence, may I kindly ask for guidance or step by step solutions of how to solve this issue so that I can split the ligand SDF file successfully without encountering any errors? Thank you so much for your help in advance

2

This is not a gromacs related questions. anyhow, try spling it by not considring the sterochemistry may work, or use a single script to split the chain using RDkit.

3

Alright, noted. Thank you @scinikhil for the reply and help. Really appreciate it.