From: Stober, Spencer T (spencer.t.stober_at_exxonmobil.com)
Date: Wed Apr 19 2017 - 10:44:18 CDT
Yes, this was indeed fixed by one of the website owners. Thanks.
Best regards, Spence
From: Marcelo C. R. Melo [mailto:melomcr_at_gmail.com]
Sent: Wednesday, April 19, 2017 10:40 AM
To: Stober, Spencer T
Subject: Re: namd-l: Hybrid QM/MM in NAMD 2.12 with Gaussian
I am able to reach the file from the website, so maybe someone fixed the link before I got there. Could you check again?
In any case, I have attached the file to this e-mail.
I worked on the QM/MM interface in NAMD and would be happy to hear any feedback you would like to give. Because of the response from some users, the next release will already come with a couple of new features.
Marcelo Cardoso dos Reis Melo
University of Illinois at Urbana-Champaign
+1 (217) 244-5983
On 18 April 2017 at 10:24, Stober, Spencer T <spencer.t.stober_at_exxonmobil.com<mailto:spencer.t.stober_at_exxonmobil.com>> wrote:
I cannot access the hyperlink to the NAMD QM/MM interface script for GAUSSIAN, although the NAMD website seems to indicate that it exists. Please see below.
In the website describing the new Hybrid QM/MM in NAMD 2.12:
In this paragraph:
“Two examples of python scripts can be found here (ORCA<http://www.ks.uiuc.edu/Research/qmmm/Scripts/runORCA.py> , GAUSSIAN<http://www.ks.uiuc.edu/Research/qmmm/Scripts/run_gaussian.py> ), with comments explaining the format in which NAMD will write data for the QC software, and the format in which NAMD expects to find the results. This script wraps ORCA (which is natively supported) and GAUSSIAN as examples and templates for the utilization of other software. We will soon make scripts available to other QC codes, including TeraChem, Q-Chem, CPMD, among others.”
In the above, there are two hyperlinks one for the ORCA python script (http://www.ks.uiuc.edu/Research/qmmm/Scripts/runORCA.py), and one for an example using GAUSSIAN (http://www.ks.uiuc.edu/Research/qmmm/Scripts/run_gaussian.py). Unfortunately, the hyperlink leading to run_gaussian.py is not working.
Hopefully, one of you has this file or can address the broken link on the website. Thanks in advance.
Best regards, Spence
Spencer T. Stober, Ph.D.
Corporate Strategic Research
ExxonMobil Research and Engineering
1545 Route 22 East
Annandale, NJ 08801
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