Two things
first, you can use the EXTERNAL module inside amber itself, that will
hokk you up with gaussian
In this way, you can figure out what part is QM, which part is MM for
the electrostatic potential, etc.
If not, gaussian has a way to read external charges. So, you would write
a pdb file from amber, and then you need to convince gaussian who are QM
atoms and which ones are classical charges.
Adrian
On 7/5/16 2:17 PM, Jason Swails wrote:
> I'm not quite clear what you're wanting. I can think of 2 things:
>
> 1. The ESP from each non-QM atom in the system on the QM atoms so you can
> provide that as input to Gaussian?
>
> If this is the case, you can just add point-charges to the Gaussian input
> file directly that correspond to each atom outside the QM region instead
> and Gaussian will do that for you.
>
> 2. The ESP on each atom from the combined QM/MM Hamiltonian?
>
> I think you can just use the Gaussian cube file that you can generate from
> the QM calculation to compute this directly from the resulting
> wavefunction/electron density. (I did it a long time ago, and can't
> remember all of the details).
>
> HTH,
> Jason
>
> On Tue, Jul 5, 2016 at 12:20 PM, Elisa Pieri <elisa.pieri90.gmail.com>
> wrote:
>
>> Yes, sorry, I took it for granted. I'm talking about electrostatic
>> potential!
>>
>> Elisa
>> Il 04/lug/2016 18:23, "Adrian Roitberg" <roitberg.ufl.edu> ha scritto:
>>
>>> Hi Elisa
>>>
>>> Can you clarify what you mean by 'potential on each atom' means?
>>>
>>> You can take a snapshot from amber, convert those coordinates to a
>>> format gaussian understand and compute whatever you want with gaussian
>>> itself. Not sure what you mean by the 'potential' here.
>>>
>>> adrian
>>>
>>>
>>>
>>> On 7/4/16 10:43 AM, Elisa Pieri wrote:
>>>> Dear all,
>>>>
>>>> I'm taking snapshots of a peptide from an Amber trajectory, I need to
>>>> perform energy calculations on each geometry using Gaussian. In order
>> to
>>>> proceed in my calculations, I need to know the potential on each atom
>> of
>>> my
>>>> peptide. How can I get this information?
>>>>
>>>> Elisa
>>>> _______________________________________________
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>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>> --
>>> Dr. Adrian E. Roitberg
>>> University of Florida Research Foundation Professor.
>>> Department of Chemistry
>>> University of Florida
>>> roitberg.ufl.edu
>>> 352-392-6972
>>>
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>> _______________________________________________
>> AMBER mailing list
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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
--
Dr. Adrian E. Roitberg
University of Florida Research Foundation Professor.
Department of Chemistry
University of Florida
roitberg.ufl.edu
352-392-6972
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Received on Tue Jul 05 2016 - 11:30:03 PDT
