Hi All,
I am trying to reduce my trajectory size so that I can visualize the same
using VMD. I tried following steps:
1) Striping of water from trajectories
trajin prod.mdcrd 1 500 1
trajout traj_no_wat.mdcrd mdcrd
strip :WAT
strip :Cl-
2) New Topology File generation:
.rst file from production run --> use of ambpdb command to generate the pdb
file --> striping of water and ions from the generated pdb file
(protein-ligand complex only)
3) use of tleap to generate new topology ( prod_nowat.prmtop) file for the
ion and water stripped complex. The new files are successfully geneated
without any error.
Now I am trying to visualize the no_wat.mdcrd and prod_nowat.prmtop in VMD.
I am getting unusual bonds in the structures. Please suggest me the
correction required??
Thanks
Hirdesh
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Received on Sat Jan 14 2012 - 06:30:03 PST
