VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Fri Aug 01 2008 - 15:24:51 CDT

Hi Jianhui,
could you verify that you tried the pbc wrapping on a fresh copy of your
trajectory (not one that had been previously broken by rewrapping) each
time? Failing that, could you send your structure and a couple frames
that need wrapping so I can have a look?
Best,
Peter

Jianhui Tian wrote:
> Hi Peter,
>
> I have tried -compound chain / res / segment. All of them still give
> wired bond connections. (It's a small peptide on the edge of the
> wrapped new unit cell.) Is there anything that I can have done
> wrong? I have read the manual carefully, but can't find any other hint
> to solve the problem. I dont know whether I missed something. Thanks.
>
> Jianhui
>
> On 8/1/08, *Peter Freddolino* <petefred_at_ks.uiuc.edu
> <mailto:petefred_at_ks.uiuc.edu>> wrote:
>
> Hi Jianhui,
> try using the -compound option to enforce wrapping groups together
> (see the manual page for the possible options; generally -compound
> res works well if you're just worried about broken waters,
> -compound chain otherwise).
> Best,
> Peter
>
>
> Jianhui Tian wrote:
>
> Hi,
> I used pbctools to wrap my system for better visualization.
> The command I used is {pbc wrap -center "resid 1" -all}.
> After all is finished, I see broken molecules, which means the
> whole molecule is on the edge of the new box, half of the
> molecule is on one side and half on the other side and wired
> bond connecting them. How can I avoid such broken molecules?
> Jianhui
> Biocomputation
> Rensselar Polytechnic Institute
>
>