does it change if the trajout is after the strip command?
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 - 12:30:08 PDT
