I chose the file type Amber coordinates. I think this file type loads mdcrd without the box option.
Jaya.
On 05/12/10, Jason Swails <jason.swails.gmail.com> wrote:
>
> 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) (
> > http://www.simmerlinglab.org) (http://www.simmerlinglab.org%29)
> > > > ===================================================================
> > > >
> > > > _______________________________________________
> > > > AMBER mailing list
> > > > AMBER.ambermd.org
> > > > http://lists.ambermd.org/mailman/listinfo/amber (http://lists.ambermd.org/mailman/listinfo/amber) (
> > http://lists.ambermd.org/mailman/listinfo/amber) (http://lists.ambermd.org/mailman/listinfo/amber%29)
> > > >
> > >
> > >
> > >
> > > --
> > > 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) (
> > http://lists.ambermd.org/mailman/listinfo/amber) (http://lists.ambermd.org/mailman/listinfo/amber%29)
> > >
> >
> >
> >
> > _______________________________________________
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> > 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
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber (http://lists.ambermd.org/mailman/listinfo/amber)
>
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Received on Wed May 12 2010 - 13:30:05 PDT
