VMD-L Mailing List

From: WT Ren (renerwei_at_gmail.com)
Date: Sun Jun 30 2019 - 20:58:24 CDT

Dear Mariano:

Thanks very much for your reply. I uploaded the files to google drive.
The initial pdb structure was constructed by Molefacture.
I forgot to mention that in the QM calculation, water in one trajectory
moved away from the binding site, so I excluded this trajectory
during the MM/QM optimization("BPG-DON-H3.log").

Best regards
Weitong Ren
https://drive.google.com/file/d/1bGNKnq9TMh4pXSHEQNADTiPM6emeT5mT/view?usp=sharing

On Mon, Jul 1, 2019 at 1:01 AM mariano spivak <mariano_at_ks.uiuc.edu> wrote:

> 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.
>>
>