This is very similar to several other emails you've sent recently, so
perhaps it'd be helpful to provide a general answer. ptraj (and likewise
cpptraj) is a very flexible program capable of outputting structures to a
number of different formats, including PDB files.
Furthermore, any modification you make to your system prior to using the
*trajout* command will be reflected in the coordinates and atoms printed out
(for instance if you strip certain atoms according to a mask, those will not
be printed).
Thus, the actions that you should do prior to your trajout commands are
*just* those that you want done to the coordinates in your final output
files (there's no need to ask us what you want done).
Furthermore, no information (like box information) that's not present in a
specific output format (i.e. PDB) will be force-fed into that format if
present in ptraj.
As a general strategy, one way of outputting specific atoms that you *want*
is to create a mask for those atoms (use ambmask to help you figure out if
your mask is really what you want!), then strip that mask negated with !.
For instance, suppose you only wanted the lysine residues, then your mask
would be :LYS. To keep just your lysine residues, you would then strip
!:LYS.
Try to understand the Amber mask syntax, and use the ambmask program to help
you determine if your mask is what you think it is.
HTH,
Jason
On Fri, Aug 12, 2011 at 2:34 AM, Catein Catherine <askamber23.hotmail.com>wrote:
>
> 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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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Fri Aug 12 2011 - 04:30:02 PDT
