VMD-L Mailing List

From: Adupa Vasista (adupavasista_at_gmail.com)
Date: Wed Jan 29 2020 - 09:34:57 CST

Great. Thank you

On Wed, Jan 29, 2020 at 8:28 PM David Sáez <davidsaezsan_at_gmail.com> wrote:

> 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.*
>>
> 

-- 
*A.VasistaM.Tech,Department Of Chemical Engineering,*
*IIT Guwahati.*