Hi,
You need to generate a topology file that matches the stripped system.
You could probably do this in leap, although I'm not sure if there is
an easy way to tell leap to get rid of hydrogens.
You could also generate a topology that matches your stripped system
with cpptraj:
cpptraj 1csad.top << EOF
trajin mdcrd
strip .?H* outprefix strip
EOF
This will generate an Amber topology file of the stripped system named
"strip.1csad.top" that can be used to visualize the stripped
trajectory and perform further analysis. Note however that the
topology is not complete and cannot be used for further MD.
Let me know if you have any more questions.
-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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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Wed Jul 27 2011 - 06:30:03 PDT
