VMD-L Mailing List

From: Ern Ong (Ern.Ong_at_student.adfa.edu.au)
Date: Wed Jul 26 2017 - 01:40:49 CDT

Hi VMD users,

I have performed a series of optimization on a neutral pyruvate group + beta-D-mannose with Gaussian 09 program and ffTK plugin in VMD 1.9.3 (for WIN32 30Nov2016). Currently I wish to run simulations with a charged pyruvate group (COO-) + beta-D-mannose, I would like to know whether I should proceed to dihedral optimization? I have done the charge optimization with HF/6-31G theory for the charged pyruvate group (COO-) + beta-D-mannose. Not sure whether the results can be affected if I use the dihedral parameters that I got from the optimization of neutral pyruvate group + beta-D-mannose.

Thank you.

Best Regards,

Ernest Ong Ern Seang

PhD student
School of Engineering and Information Technology (SEIT)
University of New South Wales@ ADFA
NorthCott Drive, Campbell
ACT 2600, Australia.