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: www.awgoetz.de<http://www.awgoetz.de>
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 - 13:30:02 PDT
