Error while running Vina for multiple ligand docking

[mbilaltayyab]

i am trying to run pearl script on Ubuntu linux subsystem running on Windows11 to do multiple ligand docking but getting an error "An internal error occurred in ../../../src/lib/tree.h(101)."

the script which i am using is in following "

!/usr/bin/perl

print"Ligand_file:\t"; $ligfile=; chomp $ligfile; open (FH,$ligfile)||die "Cannot open file\n"; @arr_file=;

for($i=0;$i<@arr_file;$i++) { print"@arr_file[$i]\n"; @name=split(/./,@arr_file[$i]); } for($i=0;$i<@arr_file;$i++) { chomp @arr_file[$i]; print"@arr_file[$i]\n"; system("vina --config conf.txt --ligand @arr_file[$i]");

Kindly help me to rectify it if anyone find a solution for it.

[diogomart]

Can you post the ligand and conf.txt?

[mbilaltayyab]

conf.txt 12.8.xlsx

[diogomart]

Would have to look at the actual ligand and receptor PDBQT to see what's going on.

[pamochi]

Having the exact same problem. Same script, similar setup. Reinstalled Vina and AutodockTools, no difference

[pamochi]

@mbilaltayyab Did you convert your ligands from SMILES to pdbqt? I had done that before and gotten the same error, just downloaded my ligands again as SDF this time, added charges, converted 3d, minimized energy, converted to mol2 then pdbqt. And it seemed to work

[diogomart]

@pamochi can you post the input files and all parameters and options so i can reproduce on my end?

[pamochi]

@diogomart I managed to fix the issue on my end. I had the same scirpt and config as @mbilaltayyab. I switched over to my Ubuntu VM and with a bash script also had the same error

So, I went back and instead of converting my SMILES to pdbqt, I converted SDFs. And it seemed to work. Originally I used "$ obabel -i smi smiles.smi -o sdf -O out.sdf -m -h --gen3d" to convert my SMILES

And now I am using "for i in .sdf; do obabel $i -O $i -h; done" "for i in .sdf; do obabel $i -O $i --gen3d; done" "for i in .sdf; do obminimize -ff MMFF94 -n 1000 $i; done" "obabel .sdf -omol2 -m" "obabel *.mol2 -opdbqt -m"