Dear Francesca,
Also, you can try with PUPIL as a tightly coupled software to
AMBER, which is also is able to work as AMBER/PUPIL/NWChem interface in
both serial and parallel MPI executions.
You can found more information within the Amber manual and in the
sourceforge webpage:
http://pupil.sourceforge.net/
Best regards,
Joan
El 19/6/19 a les 9:21, Francesca Lønstad Bleken ha escrit:
> Hi,
>
> Yes, I have read the amber manual for the QMMM, however it has very little information on
> NWChem specifically. While there is a subsection for the other QM-codes implemented, I did not find this for
> NWChem. I am asking if there is any other information available for NWChem/Amber specifically beyond what is available in the
> Manual. For instance there is an input template for the other codes, but not for NWChem. I would be very interested in
> getting more info towards this. I have received a very kind answer from the authors of the article I mentioned saying that they are working on
> making documentation. While this is extra to what is currently shipped with Amber, and I was hoping for some more on the available implementation.
>
> Best regards,
> Francesca
>
>
> Date: Tue, 18 Jun 2019 12:50:15 -0400
> From: "James Kress" <jimkress_58.kressworks.org>
> Subject: Re: [AMBER] QMMM, with NWChem and Amber
> To: "'AMBER Mailing List'" <amber.ambermd.org>
> Message-ID: <004001d525f5$e80b2f40$b8218dc0$.kressworks.org>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Did you read the AMBER manual? Discussion of using NWChem starts on page
> 157 of the Amber18 pdf version of the manual.
>
> A search of the manual will provide additional information.
>
> Jim
>
>
> -----Original Message-----
> From: Francesca L?nstad Bleken <francesca.l.bleken.sintef.no>
> Sent: Tuesday, June 18, 2019 8:04 AM
> To: amber.ambermd.org
> Cc: Francesca L?nstad Bleken <francesca.l.bleken.sintef.no>
> Subject: [AMBER] QMMM, with NWChem and Amber
>
> Dear Amber community,
>
> I have found an article and a corresponding thesis with a QMMM
> implementation for Amber with NWChem.
> I have am having problems following the procedure written out in the thesis,
> and am wondering if there is anyone out there with NWChem+ Amber experience.
> I have written to the corresponding author of the article, but it might also
> be worthwhile to approach this knowledgeable list.
> The article in question is:
> Combined Quantum-Mechanical Molecular Mechanics Calculations with NWChem and
> AMBER: Excited State Properties of Green Fluorescent Protein Chromophore
> Analogue in Aqueous Solution, J. Comp. Chem. 2017, 38, 1631 and the thesis
> is found here: https://escholarship.org/uc/item/08z3x8mc
>
> A tutorial, some sample input scripts or anything like that would be greatly
> appreciated! Especially since the NWChem section in the AMBER18 manual still
> is not very developed.
>
> I have found the following tutorials, but neither of these deal with the
> implementation with external QMcodes (NWChem in particular)
> http://ambermd.org/tutorials/advanced/tutorial2/section3.htm
> https://github.com/CCPBioSim/qmmm_workshop
>
> I also have question about the mailing list, is it possible to se it up to
> receive e-mails separately and not as a daily batch (this could be useful
> when I am in the middle of a discussion)?
> I looked in the section on editing options and I did not see this as a
> possibility. I will be glad for a correction if I am wrong.
>
> Best regards,
> Francesca
>
>
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> AMBER mailing list
> AMBER.ambermd.org
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Received on Wed Jun 19 2019 - 07:00:03 PDT
