VMD-L Mailing List

From: mariano spivak (mariano_at_ks.uiuc.edu)
Date: Sun Jun 30 2019 - 11:01:20 CDT

Hi,

I can check your files to see what is the problem. You can send me the
files in a separate email.
It sounds like you are including water molecules from your pdb/xray
structure in the FFTK framework, which is not needed.

Best

Mariano Spivak, Ph.D.

Theoretical and Computational Biophysics Group

Beckman Institute, University of Illinois.

mariano_at_ks.uiuc.edu

mspivak_at_illinois.edu

On Sun, Jun 30, 2019 at 10:06 AM WT Ren <renerwei_at_gmail.com> wrote:

> Dear All:
>
> I have been struggling to optimize the partial charges of one small
> molecule obtained from CHARMM-GUI by fftk and gaussian for several days. I
> followed the workflow in the tutorial, but unfortunately, the MM/QM
> distances and energies did not converge. Some water molecules moved far
> from the interaction site. I tried excluding those water molecules from the
> optimization, then other water molecules would move away. It seems there
> are some tricks in the charge optimization. Could anyone give me some
> advice or tips on this issue. I will be very grateful for any guidance. I
> can send the files if they would help.
>
> PS: The ligand molecule includes two phosphates and carries -4 charges.
>