One other thing just occurred to me - your output trajectory might
have box coordinates in it since you didn't specify "nobox" to ptraj.
Are you loading the trajectory as "Amber Coordinates with Periodic
Box"?
-Dan
On Wed, Jul 27, 2011 at 8:23 AM, Devlina Chakravarty
<devlina.chakravarty.gmail.com> wrote:
> Hi,
> I am trying to strip all hydrogen from the trajectory files in ptraj before
> converting into a single crd file. The input file is
>
> ptraj 1csad.top << EOF
> trajin 1csad-equil-traj.crd
> trajin 1csad-md-traj.crd
> trajin 1csad-md-traj1.crd
> trajin 1csad-md-traj2.crd
> strip .?H*
> rms first :20-410.CA
> trajout md-10ns-noh.crd
> EOF
>
> It seems to be working fine but I am trying to load the same in vmd I am
> getting a very strangely deformed protein (I am loading it on a pdb file
> which I got after minimisation and contains no Hydrogen in vmd)
>
> Is there a problem with the crd file itself or maybe I am going wrong when
> loading in vmd, I am at a loss. Any help would be appreciated.
>
> Thanks in advance,
> --
> Devlina Chakravarty
> JRF
> Bose Institute
> Kolkata
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> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Wed Jul 27 2011 - 06:30:04 PDT
