VMD-L Mailing List

From: René Hafner TUK (hamburge_at_physik.uni-kl.de)
Date: Tue Jan 25 2022 - 01:25:13 CST

Hi Aditi,

you may give https://urldefense.com/v3/__https://github.com/jhenin/qwrap__;!!DZ3fjg!uMEYixtHuzgxo6GZREOxaXrL2oABKpjbyj1mD8PDAV0HmehDxaJdW8ErRYhQ26F2YQ$ a try. (But I don't expect
it to solve the problem)

However maybe the ligand is actually leaving/entering a pocket multiple
times and the periodic box might just be too small such that the ligand
gets wrapped?

Kind regards

René

On 1/25/2022 7:11 AM, Aditi Gotkhindikar wrote:
>
>
> ---------- Forwarded message ---------
> From: *Aditi Gotkhindikar* <aditi.got_at_gmail.com>
> Date: Mon, Jan 24, 2022 at 12:04 PM
> Subject: vmd-l: pbc wrap issue
> To: VMD Mailing List <vmd-l_at_ks.uiuc.edu>
>
>
> Hello,
> I have a dcd file of a protein-ligand simulation . I am facing the
> problem of pbc wrap. The ligand is moving in and out of protein in the
> overall time period.
> I tried the command below but couldn't solve the problem.
> command -
> 1. pbc wrap -centersel "protein" -center com -compound residue -all
>
> Please can you suggest a solution to the problem.
>
>
> Thank you
> Aditi
>
>
> 

-- 
--
Dipl.-Phys. René Hafner
TU Kaiserslautern
Germany