I would like to assign charge to heme iron center, for some reason the MVT assigns zero charge to it.
Can anyone explain to me how autodock vina deals with electrostatic interactions? From what I understand , vina ignores charges. Is that true?
Can anyone suggest a way to do molecular simulation and check the structure whether it is correct or not?
Hi,
While working with autodock, it adds the charges as a part of the protocol and shows as the warning box. Molecular simulation is a huge concept with diverse uses, it depends on the system you are performing on. Basic eg could be like mimicking the behavior of protein in water using softwares NAMD and VMD and to analyse the structure after simulation there are again different criteria, easy one could be checking the RMSD of the simulated structure. Hope this helps.
Regards
- Badges
- Science topic
- Similar topics
- Filing