VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Fri Aug 01 2008 - 16:29:59 CDT

On Fri, 1 Aug 2008, Peter Freddolino wrote:

JH> Hi Jianhui,
JH> could you verify that you tried the pbc wrapping on a fresh copy of your
JH> trajectory (not one that had been previously broken by rewrapping) each

... furthermore you may want to set the center of the wrapping
cell to a selection with your protein using the -center flag
or some other appropriate choice.

cheers,
   axel.

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

-- 
=======================================================================
Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
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If you make something idiot-proof, the universe creates a better idiot.