AMBER Archive (2003)

Subject: question about partial charge

From: yuann (yuann_at_bioinfo.ndhu.edu.tw)
Date: Mon Feb 17 2003 - 20:43:48 CST

Dear Amber user,
  Should I assign partial charges after Gaussian98 calculation or simply
  use the formal charge when dealing with the metal ions in protein, such
  as zinc, potassium and magnesium,... etc.

  I also want to do a optimization calculation with HF/6-31g* function on
  an organic molecule with two identical structure to obtain its partial
  charge. The initial structure is extracted from a complex structure
  stored in PDB.
  Unluckily, this organic molecule is too large to do optimization
  job in Gaussian98 even though I sent this job to my server, IBMP690,
  with 16CPU. So, is it reasonable to simply do optimization job on only
  one structure of this dimer or just do general job without optimizaion
  on a whole dimer in order to get its ESP for RESP fitting?

  Thanks for your suggestion!

Best Regards,

sychen.