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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Received on Wed Jun 19 2019 - 00:30:02 PDT
