PBC and Alignment issues

From: Angel Tamez (tameza_at_duq.edu)
Date: Wed Apr 20 2022 - 16:03:33 CDT

Hi, I have a problem with VMD wrap and alignment. I simulated a docked RNA and protein complex, but when I wrap the complex using this command:
pbc wrap -center com -centersel “nucleic" -compound residue -all
pbc wrap -center com -centersel “nucleic" -compound fragment -all
and more...
For the most part the wrapping portion works, with some frames having the complex as monomers at either end of the box.
However, when I align the complex for further analysis, the protein, or nucleic acids, or both go to one end of the box.
How would I best remedy this issue?
Thank you very much
Angel Tamez
Graduate Student
NSF-Graduate Research Fellow
600 Forbes Ave
Duquesne University
308 Mellon Hall
Pittsburgh, PA
E: tameza_at_duq.edu<mailto:tameza_at_duq.edu>

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