vmd can't load the traj file directly, so you need to tell us how you
generated the prmtop or pdb that you used in vmd prior to loadingthe
traj file. it should be exactly what you made in ptraj- same system
but no water and no periodic box.
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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Received on Wed May 12 2010 - 12:30:03 PDT
