Can you provide the ligand files you used, or can you suggest some of website which provides the ligand libraries for free specially for natural compounds..
I have optimised my ligand with Marvin sketch and added gasteier charge, even there comes an error that there is no atomic partial charge on ligand,can u plz give me any solution
@aarchna_yadav I've saw similar errors in PDB files. I used spdbv software back then. It has an option; select all the atoms then Tools --> Fix Selected Side Chains --> Quick and Dirty. After that save the current layer into a new file. I think it might help.
After copying babel.exe, use this: babel.exe *.sdf -opdbt -m *.sdf implicates all files containing .sdf string. -opdbqt defines the format of the outputs . And -m is for spiting.
Can you provide the ligand files you used, or can you suggest some of website which provides the ligand libraries for free specially for natural compounds..
You can use Drugbank, LifeChemicals, ASINEX, and ZINC natural product databases. These are very helpful.
I have optimised my ligand with Marvin sketch and added gasteier charge, even there comes an error that there is no atomic partial charge on ligand,can u plz give me any solution
@aarchna_yadav I've saw similar errors in PDB files. I used spdbv software back then. It has an option; select all the atoms then Tools --> Fix Selected Side Chains --> Quick and Dirty. After that save the current layer into a new file. I think it might help.
Please provide the command code.. Thanks in advance..
After copying babel.exe, use this: babel.exe *.sdf -opdbt -m
*.sdf implicates all files containing .sdf string. -opdbqt defines the format of the outputs . And -m is for spiting.
@@al1r3z49 thanks a lot..
Sir, Can we use the pdbqt files for pyrx software also?
Sorry for my late answer. Yes you can, I think it has also tools for analyzing docking interactions too.