sdf file problem

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sdf file problem

Postby mai el-naggar » Fri Dec 13, 2013 8:42 pm

I am doing docking using autodock vina in pyrx 0.8
when I did docking for a known compound using its 3D sdf file downloaded from pubchem and I used also other sdf file for the same compound but constructed by chem 3D ultra and saved as sdf file, both resulted in the same docking score, but they are not superimposed and they show different H-bonding in visualization.
should not they (the same models of the same compound with different sdf files) be superimposed? what is the problem here?
Thanks in advance
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Re: sdf file problem

Postby sargis » Sat Dec 14, 2013 8:48 pm

Thank you for using PyRx. I don't understand what seems to be the problem here. Different poses can have the same docking score. Why should they (the same models of the same compound with different sdf files) be superimposed? Perhaps you can upload screenshots and output/logs files to clarify this topic.
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Re: sdf file problem

Postby mai el-naggar » Sat Dec 14, 2013 11:40 pm

I mean that the docking results should be accurate and reproducible each time when using the same conditions for the same compound, whatever what is the source of the sdf file used for docking.
For analyzing docking results we not depend only on the docking score, we also use visualization to detect the H-bond interactions between the ligand and the receptor.
I did docking for a known compound (6-gingerol) twice in the same docking process, once using 3 D sdf file downloaded from pubchem (CID 442793) and I used also other sdf file for the same compound constructed by chem 3 D ultra. after docking both sdf files produced the same highest docking score for the first model, but they showed different interaction with the receptor. sdf file constructed by chem 3 D showed better interaction.
should not both sdf files produce the same docking score and the same receptor-ligand interaction patern for each produced docking model?
should we do any modification for the ligand when using sdf file other than minimizing energy and converting it to autodock ligand to convert it to pdbqt file?
I hope that the topic is clarified.
Thank you
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Re: sdf file problem

Postby sargis » Sun Dec 15, 2013 4:19 am

mai el-naggar wrote:I mean that the docking results should be accurate and reproducible each time when using the same conditions for the same compound, whatever what is the source of the sdf file used for docking.
For analyzing docking results we not depend only on the docking score, we also use visualization to detect the H-bond interactions between the ligand and the receptor.
I did docking for a known compound (6-gingerol) twice in the same docking process, once using 3 D sdf file downloaded from pubchem (CID 442793) and I used also other sdf file for the same compound constructed by chem 3 D ultra. after docking both sdf files produced the same highest docking score for the first model, but they showed different interaction with the receptor. sdf file constructed by chem 3 D showed better interaction.
should not both sdf files produce the same docking score and the same receptor-ligand interaction patern for each produced docking model?

Thanks for the clarification. I see what you mean now. No, both sdf files can produce different docking score and receptor-ligand interaction pattern. Even with identical sdf files you can get different docking results. See http://vina.scripps.edu/manual.html#faq under Why is my docked conformation different from what you get in the video tutorial?

mai el-naggar wrote:should we do any modification for the ligand when using sdf file other than minimizing energy and converting it to autodock ligand to convert it to pdbqt file?

Not unless you have a specific reason to do so. Perhaps someone else can provide more detailed answer here.
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