Hi,
Try selecting type:crd on VMD, since u stripped water and used nobox
flag on ptraj, there is no box information on your new trajectory anymore.
I hope this helps,
Asim
xueping wrote:
>Dear all,
>
>I use ptraj to combine my mdcrd files, below is my
>script:
>
>trajin ../PfCo.md_1.mdcrd
>trajin ../PfCo.md1.mdcrd
>trajin ../PfCo.md2.mdcrd
>trajin ../PfCo.md3.mdcrd
>trajin ../PfCo.md4.mdcrd
>trajin ../PfCo.md5.mdcrd
>trajout PfCo_nowat.mdrcd nobox
>rms first out PfCo.rmsfit .CA time 0.1
>center :1-295
>image familiar
>strip :WAT
>
>Then, i load the PfCo_nowat.mdrcd file to VMD, and
>choose type:crdbox after loading my prmtop file
>without water. The structure loaded look so weird, it
>has alot of long lines and it doesn't look ok....
>
>So, i check my mdcrd file one by one, loading it in
>VMD with the prmtop file with water, and it look ok
>for all the mdcrd files...
>
>Is it because of my ptraj script? It is same to my
>average structure that i produce using ptraj, the
>structure look so weird. Please give me some
>suggestions. Thank you very much.
>
>Regards
>xueping
>
>
>
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Received on Thu Apr 07 2005 - 06:53:00 PDT
