Dear Sir/Madam,
I would like to extract only selected atoms or backbone atoms of a protein from a trajectory to PDB format.
How can I do it with Ptraj? Lets say how to modify the following ptraj file to extract only CA and CB atoms for each residues?
#trajin ../xxx.mdcrd.gz
#-- put all the pdb frames in a subdirectorytrajout PDB/xxx.pdb pdb nobox nowrapstrip :WATstrip :Na+
On more question on this ptraj file. My xxx.mdcrd.gz is the trajectory comes from a MD with periodic boundary and explicit solvent, is it correct to use nobox and nowrap when I extract them to pdb format?
Best regards,Catherine
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Received on Fri Aug 12 2011 - 00:00:03 PDT
