Make sure the choice of VMD plugin you chose was correct for your system.
You specified nobox in the ptraj script, so make sure you are loading the
mdcrd without the "box" option for Amber trajectories.
Good luck!
Jason
On Wed, May 12, 2010 at 3:56 PM, Jayalakshmi Sridhar <jsridhar.xula.edu>wrote:
>
> After putting the trajout statement after the strip command, I do not see
> the box shape. The number of frames are also consistent with 2400 frames.
> But the atoms are still streaking in the vmd display. I am attaching a
> picture of the image as jpg file.
> Jaya.
>
> On 05/12/10, Jason Swails <jason.swails.gmail.com> wrote:
> >
> > On Wed, May 12, 2010 at 3:22 PM, Carlos Simmerling <
> > carlos.simmerling.gmail.com> wrote:
> >
> > > does it change if the trajout is after the strip command?
> > >
> >
> > I believe yes. Once it trajouts, I think it just stops (so nothing after
> > the trajout is processed). Jaya, try putting the trajout statement last.
> >
> > Good luck!
> > Jason
> >
> >
> > >
> > > On 5/12/10, Jayalakshmi Sridhar <jsridhar.xula.edu> wrote:
> > > > Dear Amber Users,
> > > > I have run MD on my protein for 12ns. I was able to combine all the
> MD
> > > > trajectories into one .binpos file. When I try to image the protein
> using
> > > > ptraj, I run into problems. The output .mdcrd does not load well in
> VMD.
> > > The
> > > > atoms seem to be streaking all over the box. The ptraj script I used
> is
> > > > given below: ANy help to resolve this problem is greatly appreciated.
> > > > Thanks.
> > > > Jaya.
> > > >
> > > > trajin ../2ns_md/2a6_md2.mdcrd 1 500 25
> > > > trajin ../2ns_md/2a6_md3.mdcrd 1 500 25
> > > > trajin ../2ns_md/2a6_md4.mdcrd 1 500 25
> > > > trajin ../2ns_md/2a6_md5.mdcrd 1 500 25
> > > > trajin ../2ns_md/2a6_md6.mdcrd 1 500 25
> > > > trajin ../2ns_md/2a6_md7.mdcrd
> > > > trajin ../2ns_md/2a6_md8.mdcrd
> > > > trajin ../2ns_md/2a6_md9.mdcrd
> > > > trajin ../2ns_md/2a6_md10.mdcrd
> > > > trajin ../2ns_md/2a6_md11.mdcrd
> > > > trajin ../2ns_md/2a6_md12.mdcrd
> > > > trajin ../2ns_md/2a6_md13.mdcrd
> > > > trajin ../2ns_md/2a6_md14.mdcrd
> > > > trajin ../2ns_md/2a6_md15.mdcrd
> > > > trajin ../10ns_md_ht/2a6_md18.mdcrd
> > > > trajin ../10ns_md_ht/2a6_md19.mdcrd
> > > > trajin ../10ns_md_ht/2a6_md20.mdcrd
> > > > trajin ../10ns_md_ht/2a6_md21.mdcrd
> > > > trajin ../10ns_md_ht/2a6_md22.mdcrd
> > > > trajin ../10ns_md_ht/2a6_md23.mdcrd
> > > > trajin ../10ns_md_ht/2a6_md24.mdcrd
> > > > trajin ../10ns_md_ht/2a6_md25.mdcrd
> > > > trajin ../10ns_md_ht/2a6_md26.mdcrd
> > > > trajin ../10ns_md_ht/2a6_md27.mdcrd
> > > > trajin ../10ns_md_ht/2a6_md28.mdcrd
> > > > trajin ../10ns_md_ht/2a6_md29.mdcrd
> > > > trajin ../10ns_md_ht/2a6_md30.mdcrd
> > > > trajin ../10ns_md_ht/2a6_md31.mdcrd
> > > > trajin ../10ns_md_ht/2a6_md32.mdcrd
> > > > trajin ../10ns_md_ht/2a6_md33.mdcrd
> > > > trajout 2a6_md_2_33.mdcrd nobox
> > > > center :1-465 mass origin
> > > > image origin center
> > > > rms first mass out rms_to_first.data :1-465
> > > > average avg.pdb :1-465 pdb
> > > > strip :WAT
> > > > go
> > > >
> > > >
> > > >
> > > >
> > >
> > >
> > > --
> > > ===================================================================
> > > Carlos L. Simmerling, Ph.D.
> > > Professor, Department of Chemistry
> > > CMM Bldg, Room G80 Phone: (631) 632-1336 Fax: 632-1555
> > > Stony Brook University E-mail: carlos.simmerling.gmail.com
> > > Stony Brook, NY 11794-5115 Web: http://www.simmerlinglab.org (
> http://www.simmerlinglab.org)
> > > ===================================================================
> > >
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber (
> http://lists.ambermd.org/mailman/listinfo/amber)
> > >
> >
> >
> >
> > --
> > Jason M. Swails
> > Quantum Theory Project,
> > University of Florida
> > Ph.D. Graduate Student
> > 352-392-4032
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber (
> http://lists.ambermd.org/mailman/listinfo/amber)
> >
>
>
>
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
>
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Wed May 12 2010 - 13:30:03 PDT
