Thank you so much.
________________________________
From: Goetz, Andreas <agoetz.sdsc.edu>
Sent: Thursday, April 26, 2018 9:20:23 AM
To: AMBER Mailing List
Subject: Re: [AMBER] QM/MM-MD Mulliken Charge calculation output atom name changed
The mdout file lists the QM region coordinates of your QM region selection. This includes a mapping to the MM atom number in your original prmtop/inpcrd files. The order is ascending with respect to atom number in your prmtop/inpcrd.
You can of course just visualize your QM region to see which are the atoms that you are interested in.
All the best,
Andy
—
Dr. Andreas W. Goetz
Assistant Research Scientist
San Diego Supercomputer Center
Tel: +1-858-822-4771
Email: agoetz.sdsc.edu<mailto:agoetz.sdsc.edu>
Web: https://na01.safelinks.protection.outlook.com/?url=www.awgoetz.de&data=02%7C01%7Caxt651%40miami.edu%7C1968dcc8c3d34f9f5ef808d5abb33400%7C2a144b72f23942d48c0e6f0f17c48e33%7C0%7C0%7C636603708515927065&sdata=aTqGroc1Toc8UZG%2B6cEPQ%2BOOCQ1u3qUXWOlm1M%2F0p4I%3D&reserved=0<https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.awgoetz.de&data=02%7C01%7Caxt651%40miami.edu%7C1968dcc8c3d34f9f5ef808d5abb33400%7C2a144b72f23942d48c0e6f0f17c48e33%7C0%7C0%7C636603708515927065&sdata=g6B1yQcggfYdfOBEVkm6TF5xYWBaKcuVj48CtPDP6dE%3D&reserved=0>
On Apr 26, 2018, at 11:50 AM, Thakur, Abhishek <axt651.miami.edu<mailto:axt651.miami.edu>> wrote:
Hi everyone,
Yesterday I have posted a question, where I have asked how to find charges of my TS structure from my QM/MM-MD.
Today after computing the charges I am finding that output file has made C1,C2,C3 etc to C and similar naming for for other atom.
So due to that reason it is becoming very difficult to predict which atom charge I need.
for example
Atom Element Mulliken Charge
1 C -0.206
2 H 0.073
3 C -0.096
4 H 0.028
5 H 0.080
6 C -0.197
7 H 0.034
8 H 0.076
9 C 0.688
Here you can see all H and C are having same atom name, is there any way that amber print same atom type as in trajectory file?
Any suggestion will be highly appreciated.
Thanking you,
-Abhishek
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Received on Thu Apr 26 2018 - 14:00:02 PDT
