I am attempting to convert several .sdf ligands (2D) into .pdbqt files using the Open Babel program for molecular docking. I have followed the steps below:
After completing these steps, I encountered a fragmented structure, as shown in the picture. What could be the reason for this output, and how can I rectify it? Please provide your suggestions. Thank you.
Comandline I used:
obabel -isdf *.sdf -h -osdf -O*.sdf --gen3d
obminimize -ff MMFF94 -sd -n 10000 *.sdf
obabel *.sdf -omol2 -m
obabel *.mol2 -opdbqt -m
I have not used script based method yet I have seen some people have the same problem with script as well.
Note: This problem is coming with 2D.sdf files not with the 3D.sdf files.
Hi Vikas Kumar
I believe I have encountered similar issues before as well.
Based on your figure, there are a lot of clashing atoms in your mol2 format, hence resulting the "fractured" pdbqt format.
Here are some of my suggestions:
Hope this help. All the best.
Hello,
Have you tried using RDKit? Or converting first to PDB, then reducing and minimizing the system using Obabel?
Further, you may try with Obabel in the third step:
obabel --gen3d -isdf *.sdf -omol2 > *.mol2
Or converting first to mol2 and then minimizing them,
Good luck.
Use chem3d and upload the sdf file after that you can convert it into pdb file.
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