Date: Wed, 12 May 2010 14:56:42 -0500
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)
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
(image/jpeg attachment: vmd_ptrajimage.jpg)
- text/x-vcard attachment: Card for "Jayalakshmi Sridhar" <jsridhar.xula.edu>
