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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Received on Wed Jul 27 2011 - 05:30:03 PDT
