Re: [AMBER] Ptraj image problems

From: Jason Swails <jason.swails.gmail.com>
Date: Wed, 12 May 2010 15:30:06 -0400

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
> ===================================================================
>
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>



-- 
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 - 13:00:03 PDT
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