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Is there a difference between adding hydrogens to a molecule with...
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Agora Strange Philosophy Of War
Is there a difference between adding hydrogens to a molecule with...
Dear Veronica Mierzejewski, Good day, the hydrogen bonds and other charges like Gasteiger, Kollman charges, and Hydrogens (polar) are important for docking which are saved in pdbqt format and used as input for the rest of the process in AutoDock. Coming to your question, It is advisable to use the AutoDock to add hydrogen and save output as pdbqt, of course you can convert the hydrogens added in pdbqt format and import into AutoDock, however there is some difference in the number of hydrogens added which differs when you use PyMOL, Discovery Studio, and UCSF Chimera when I tried adding polar hydrogens using AutoDock and PyMOL. You can however convert into PDB to PDBQT using PyMOL or Chimera and use and are error free.
Dear Veronica Mierzejewski, Good day, the hydrogen bonds and other charges like Gasteiger, Kollman charges, and Hydrogens (polar) are important for docking which are saved in pdbqt format and used as input for the rest of the process in AutoDock. Coming to your question, It is advisable to use the AutoDock to add hydrogen and save output as pdbqt, of course you can convert the hydrogens added in pdbqt format and import into AutoDock, however there is some difference in the number of hydrogens added which differs when you use PyMOL, Discovery Studio, and UCSF Chimera when I tried adding polar hydrogens using AutoDock and PyMOL. You can however convert into PDB to PDBQT using PyMOL or Chimera and use and are error free.
Dear Veronica Mierzejewski, Good day, the hydrogen bonds and other charges like Gasteiger, Kollman charges, and Hydrogens (polar) are important for docking which are saved in pdbqt format and used as input for the rest of the process in AutoDock.
Coming to your question, It is advisable to use the AutoDock to add hydrogen and save output as pdbqt, of course you can convert the hydrogens added in pdbqt format and import into AutoDock, however there is some difference in the number of hydrogens added which differs when you use PyMOL, Discovery Studio, and UCSF Chimera when I tried adding polar hydrogens using AutoDock and PyMOL. You can however convert into PDB to PDBQT using PyMOL or Chimera and use and are error free.
Dear Veronica Mierzejewski, Good day, the hydrogen bonds and other charges like Gasteiger, Kollman charges, and Hydrogens (polar) are important for docking which are saved in pdbqt format and used as input for the rest of the process in AutoDock.
Coming to your question, It is advisable to use the AutoDock to add hydrogen and save output as pdbqt, of course you can convert the hydrogens added in pdbqt format and import into AutoDock, however there is some difference in the number of hydrogens added which differs when you use PyMOL, Discovery Studio, and UCSF Chimera when I tried adding polar hydrogens using AutoDock and PyMOL. You can however convert into PDB to PDBQT using PyMOL or Chimera and use and are error free.
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Venkataraghavan Ragunathan Thank you so much, this is helpful!
Venkataraghavan Ragunathan Thank you so much, this is helpful!
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