I'm on research to discover new protease inhibitor from medicinal plants via virtual screening. And I want to analyze the molecular dynamics with AMBER, but when i minimizing the ligand and macromolecule there is such problem. any suggestion can help. Thank you
Thank you for the respond. yes, i was checked the leap.log and md.out, but the step stuck in 600. while the overall of my step in the minimization state are 1000 step. My other ligands example drugs (Amprenavir) in the other folder work fine. But these chemical structure from medicinal plants that have potential to be protease HIV inhibitor, occur problems when minimization.
Please double-check your compound in terms of bond order, valence, charges, ...
Thank you for the suggestion Mr. Yoshinobu Ishikawa . Last question, if my structure looked like this. Is probably can be analyzed by molecular dynamics simulation? And what is criteria of chemical compound that can't be analyzed by molecular dynamics?
The protonation state and total charge of your compound should be important for the MDS. So you should add protons by OpenBabel with -p option like "-p 7.4". See the following link:
http://openbabel.org/docs/dev/Command-line_tools/babel.html
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