Re: wrapping a protein

From: Maxim Belkin (mbelkin_at_ks.uiuc.edu)
Date: Wed Aug 20 2014 - 17:53:46 CDT

Hi Maria,

try this:

pbc set {10 10 10} -all; # replace 10 10 10 with actual system dimensions
pbc wrap -sel "all" -all; # replace "all" with your selection

Maxim

On Aug 20, 2014, at 5:40 PM, Maria Bykhovskaia <mb.ucdelcaribe_at_gmail.com> wrote:

> Hi,
> for some reason I cannot wrap the molecule over the entire trajectory, since the command
>
> pbc wrap -all
>
> produces this error:
>
> -error Suspicious pbc side length (a=0.000000 b=0.000000 c). Have you forgotten to set the pbc parameters?
> domain error: argument not in valid range
>
> At the same time the command "pbc wrap" works (but wraps one frame)
>
> Will appreciate any insights.
> Thanks!
> Maria
>
>
> --
> Maria Bykhovskaia
> Professor and Chair, Neuroscience Department
> Director, Specialized Neuroscience Research Program
> Universidad Central del Caribe
> Bayamon, Puerto Rico
> http://maria.ucdelcaribe.org
> http://neuro.ucdelcaribe.org
> http://SNRP.uccaribe.net
>

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