VMD-L Mailing List

From: David Sáez (davidsaezsan_at_gmail.com)
Date: Wed Jan 29 2020 - 08:58:11 CST

Hi Adupa.

I am using Gaussian 16, Rev. B.01. During the Calc Bonded section of the
tutorial I needed to modify the file named qmtool_readwrite.tcl :

The line 1541:
[string match "Redundant internal coordinates found in file." $line]}

was changed to:

[string match "Redundant internal coordinates found in file.*" $line]}

The purpose of the asterisk was to match the corresponding line in
Gaussian16 output, which was slightly different from the G09 one.

Besides that, everything worked fine.

Regards.

On Wed, Jan 29, 2020 at 11:24 AM Adupa Vasista <adupavasista_at_gmail.com>
wrote:

> Can we use Gaussian16 to get log files for FFTK, because in the tutorial
> it is mentioned that we should get through Gaussian09?
>
> Please let me know
>
> Thank you.
>
>
>
> On Tue, Jan 28, 2020 at 7:49 AM Gumbart, JC <gumbart_at_physics.gatech.edu>
> wrote:
>
>> Hi David,
>>
>> You should look carefully at the dihedral scan that gives the anomalously
>> low values. There is probably some interaction that is too favorable,
>> possibly due to unrealistic charges. If you suspect that, you can modify
>> the charges to see if it makes a difference.
>>
>> Best,
>> JC
>>
>> On Jan 25, 2020, at 12:07 AM, David Sáez <davidsaezsan_at_gmail.com> wrote:
>>
>> Hello everyone,
>>
>> I am working on the parametrization of a small molecule using the superb
>> tool called FFToolkit and Gaussian 16. Up to now, it has worked great. Now,
>> in the dihedral section I am facing problems. When trying to find
>> parameters to reproduce the QM potential, I get this plot:
>>
>> https://www.dropbox.com/s/w0h6t27vs0z05ru/Selecc_024.png?dl=0
>>
>> Is it normal for the preliminary MM potential to be so high in comparison
>> to the QM potential? Should I take a look on the other elements of
>> interaction (charges, angles, bonds) because they could be raising the
>> energy too much?
>>
>> Thanks for your time.
>>
>> David.
>>
>>
>>
>
> --
>
> *A.VasistaM.Tech,Department Of Chemical Engineering,*
> *IIT Guwahati.*
>