Re: PBC and Alignment issues

From: Hrishikesh Dhondge (
Date: Thu Apr 21 2022 - 02:47:54 CDT


If you are simulating the complex (protein + RNA/DNA), then you might want
to wrap both protein and nucleic. Generally, what I prefer to do is wrap
protein and nucleic both and then unwrap the same.
I would suggest trying the following commands, you can add or remove
certain options according to your need.

pbc wrap -centersel "protein or nucleic" -center com -compound residue -all
pbc unwrap -sel "protein or nucleic"

I hope it helps.

On Wed, Apr 20, 2022 at 11:05 PM Angel Tamez <> wrote:

> 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: <>*

With regards
Hrishikesh Dhondge
PhD student,

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