Why do I get charge changes in SDF output for multi-ligand runs?
There is a known bug in eHiTS version 6.2 that can change the charge of Nitrogens or Oxygens in the SDF output of a multiple ligand screen if you are using the “-out myresults.sdf” command line option. The problem is due to a mis-calculation of the partial charges in the final writing of the output file. The problem does not affect ligand pose or score, as it happens only during the writing of the final SDF file. Workaround: The current work around is to run eHiTS multi-ligand runs without using the “-out myresults.sdf” flag and to look for the results in the file: $HOME/ehits_work/results/
