> On Jan 22, 2015, at 5:46 PM, Hadeer ELHabashy <hadeer.elhabashi.gmail.com> wrote:
>
> Is it correct to extract a pdb file from a restart file edited by ccptraj
> autoimage command as follows to correctly unwrap a protein structure
> inside a periodic water box ?
No. autoimage *wraps* a trajectory (i.e., it translates the COM of every molecule into the same unit cell).
> using the following commands
> $AMBERHOME/bin/ccptraj topology < trajin.in > ccptraj.log
>
> the trajin file
> "trajin file.res
> autoimage
> trajout file_unwrapped.res "
>
> then use the following command to extract the pdb
>
> $AMBERHOME/bin/ambpdb -p topology < file.res > file.pdb
This won’t work, and is unnecessary anyway. The trajout command above prints file.res in a mdcrd format, which ambpdb does not understand. You can trajout directly to a PDB file without going through ambpdb at all.
> what is the difference between the command autoimage and the unwrap
> commands of the ccptraj ?
They are opposites (note that “autoimage” is not a unique way to wrap molecules into a unit cell).
> Is there any way to extract unwrapped periodic pdb files directly form the
> wrapped restart file using ccptraj ?
Yes.
trajin restart_file.rst7
unwrap
trajout unwrapped.pdb
> Is there any way to unwrap many restart files with one trajin file and one
> ccptraj command?
Yes.
trajin restart_file1.rst7
trajin restart_file2.rst7
trajin restart_file3.rst7
.
.
.
unwrap
trajout unwrapped.pdb
If you want a separate PDB for each frame, change the trajout command to:
trajout unwrapped.pdb pdb multi
Or, if you launch the cpptraj interactive interpreter:
bash$ cpptraj -p <prmtop>
.
.
.
> trajin restart_file* # gets all files that start with “restart_file”
> unwrap
> trajout unwrapped.pdb
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Jan 22 2015 - 15:00:04 PST
