Re: [AMBER] Periodic image of iwrapped structure

From: Hadeer ELHabashy <>
Date: Fri, 23 Jan 2015 00:46:12 +0200

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 ?

using the following commands
$AMBERHOME/bin/ccptraj topology < > ccptraj.log

the trajin file
"trajin file.res
trajout file_unwrapped.res "

then use the following command to extract the pdb

$AMBERHOME/bin/ambpdb -p topology < file.res > file.pdb

what is the difference between the command autoimage and the unwrap
commands of the ccptraj ?
Is there any way to extract unwrapped periodic pdb files directly form the
wrapped restart file using ccptraj ?
Is there any way to unwrap many restart files with one trajin file and one
ccptraj command?

Thanks in advance

On Mon, Jan 19, 2015 at 3:04 AM, David A Case <>

> On Mon, Jan 19, 2015, Hadeer ELHabashy wrote:
> >
> > I have ran a simulation on a protein in water box with iwrapped periodic
> > boundary conditions . and I have extracted the pdb and I expected to see
> > the water box is replicating itself around the protein however I found
> part
> > of the protein is out of the water box and no surrounding water (attached
> > screen shot by VMD). So, how can I see a periodic image of the protein in
> > the water box .
> Just use the autoimage command in cpptraj, which will recenter the waters
> around your protein.
> ...good luck....dac
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Received on Thu Jan 22 2015 - 15:00:02 PST
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