can anybody help me why sometimes chimera and ligplot shows the different no. of hydrogen bonds formed between the ligands and the protein of the docked result obtained from the autodock 4.2 ?
The thresholds are different for different programs. That is why PoseView, LigPlot, Discovery Studio, Schrodinger, Chimera etc. produces different interaction diagrams. Sometimes you see a particular H-bond in PoseView generated diagram but don't see that in LigPlus diagram. Is is better to go for the dynamics and generate a time dependent interaction pattern. This way you can report statistically significant ligand contacts that were maintained for more than 30% of simulation time.
not familiar with that. In VMD, you may set up the criterion of hydrogen bonds. I think chimera and ligplot should also be ok for this function, it's pretty fundamental.
I am experiencing the same problem at the moment. The interactions with LigPlot is slightly different from what I am seeing with PyMol.
which of the outcomes should I report or how can I solve it?
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