After Autodock docking, I tried preset-ligand site for interaction in Protein-ligand.
But I cannot find any interaction.
Is that mean there is no interaction between protein-ligand?
There is log file below for docking
WARNING: The search space volume > 27000 Angstrom^3 (See FAQ)
Output will be DB02192_out.pdbqt
Detected 8 CPUs
Reading input ... done.
Setting up the scoring function ... done.
Analyzing the binding site ... done.
Using random seed: -617173320
Performing search ... done.
Refining results ... done.
mode | affinity | dist from best mode
| (kcal/mol) | rmsd l.b.| rmsd u.b.
-----+------------+----------+----------
1 -4.4 0.000 0.000
2 -3.8 29.437 30.282
3 -3.7 27.939 29.198
4 -3.6 45.368 45.805
5 -3.5 27.753 28.864
6 -3.4 14.464 16.293
7 -3.3 31.134 32.031
8 -3.3 1.472 2.559
9 -3.2 31.325 32.445
Writing output ... done.
Dear Lina,
Basically, Pymol shows only polar contacts in this mode, and it seems that your target ligand does not establish polar interactions with the receptor (at least, according to Pymol criteria for this type of interaction). I suggest you use some other tool, e.g., LigPlot or Discovery Studio Visualizer, they are both free for academic use and can detect many more interactions than Pymol.
I agree with Serhii Vakal .
Try the PLIP server: https://plip-tool.biotec.tu-dresden.de/plip-web/plip/index .
It does a much more complete analysis of different interaction types, and still allows you to visualise the results in PyMol.
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