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ccsb-scripps / AutoDock-Vina

AutoDock Vina
http://vina.scripps.edu
Apache License 2.0
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Vina flexible docking #304

Open aditya-jugade opened 2 months ago

aditya-jugade commented 2 months ago

During Vina flexible docking ligands are getting break .I have used vina_split command to split binding poses .I am attaching screenshots of same for your reference, can you help for same. Ligand--> vina One of binding poses after docking.--> vina2

diogomart commented 2 months ago

The second picture looks like protein sidechains, but the first one does not. I don't think one is the output of the other.

aditya-jugade commented 2 months ago

First one is only ligand and second structure is one of the split structure after docking with receptor.

On Fri, Apr 26, 2024, 21:38 Diogo @.***> wrote:

The second picture looks like protein sidechains, but the first one does not. I don't think one is the output of the other.

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diogomart commented 2 months ago

There is no ligand in the second picture.

rwxayheee commented 2 months ago

Hi @aditya-jugade Just in case you didn't notice this, there will be two types of output files after splitting the flexible docking output. For example, splitting the flexible docking output file in the example which contains 8 models, will produce 16 files, 8 for ligand and 8 for the flexible sidechains. They are named differently:

./vina_split 1fpu_ligand_flex_vina_out.pdbqt gives you eight 1fpu_ligand_flex_vina_out_ligand_<mode number>.pdbqt and another eight 1fpu_ligand_flex_vina_out_flex_<mode number>.pdbqt

What you showed in the picture looks like the latter type of the files, which contains only the flexible sidechains. They look broken because backbone atoms are not changing in the docking, and thus they are not reported as part of the docking outputs.