VMD-L Mailing List

From: Mayne, Christopher G (cmayne2_at_illinois.edu)
Date: Thu Jul 27 2017 - 22:52:49 CDT

Perturbations to charge, especially going from neutral to charged will likely impact dihedrals parameters. I would redo them. Also note, that when parametrizing charge species, the charge scaling should be adjusted from 1.16 down to 1.0 during charge optimization.

Regards,
Christopher Mayne

> On Jul 25, 2017, at 11:40 PM, Ern Ong <Ern.Ong_at_student.adfa.edu.au> wrote:
>
> 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.


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