Hi AMBER community,
I am working with a membrane-protein system which has numerous loops. I want to obtain the best aligned MD snapshots but only fit the helices and beta sheets and exclude the loop regions.
I have the following questions:
What is the best way to do this in cpptraj?
Should I use the ‘align’ keyword along with the atom mask for everything excluding loops ?
Also, what is the difference between the ‘align’ and ‘rms’ fit option for the above purpose?
Many thanks for your suggestions!
Best,
—
Sinjini Bhattacharjee
PhD Student
Molecular Theory and Spectroscopy
Max-Planck-Institut für Kohlenforschung
45470 Mülheim an der Ruhr, Germany
email: bhattacharjee.kofo.mpg.de<mailto:bhattacharjee.kofo.mpg.de>
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Received on Wed Jul 26 2023 - 07:00:02 PDT
