I would recommend upgrading to ptraj from AmberTools 1.4
(
http://ambermd.org/#AmberTools) which contains numerous improvements
over Amber 10 ptraj (be sure to apply all bugfixes though:
http://ambermd.org/bugfixesat.html). AT1.4 ptraj does exactly what you
want:
ptraj.in:
trajin ../run0.crd
center origin
image familiar origin
trajout file_out.traj
First 10 box lines of run0.crd:
86.147 86.147 86.147
86.141 86.141 86.141
86.131 86.131 86.131
86.147 86.147 86.147
86.161 86.161 86.161
86.162 86.162 86.162
86.163 86.163 86.163
86.143 86.143 86.143
86.144 86.144 86.144
86.150 86.150 86.150
First 10 box lines of file_out.traj:
86.147 86.147 86.147
86.141 86.141 86.141
86.131 86.131 86.131
86.147 86.147 86.147
86.161 86.161 86.161
86.162 86.162 86.162
86.163 86.163 86.163
86.143 86.143 86.143
86.144 86.144 86.144
86.150 86.150 86.150
Let me know if it still doesn't work.
-Dan
On Wed, Oct 13, 2010 at 6:15 AM, Dickson, Callum
<callum.dickson09.imperial.ac.uk> wrote:
> Dear Amber users,
>
> I have a question about processing a trajectory, run using periodic boundary conditions, with ptraj.
>
> I wish to center and image a trajectory with the following command:
>
> trajin file_in.mdcrd 1 2500 1
> center origin
> image familiar origin
> trajout file_out.traj
>
> When I use Amber 10 to perform this the resulting output trajectory loses the original box size information, instead each frame has the box size as given in the prmtop. However if I use Amber 7 the output trajectory keeps the original box size (which changes slightly with each frame as I am doing an NPT run). Is there an option with Amber 10 to keep the original box size with each frame?
>
> Kind regards,
> Callum Dickson
>
>
> Phd Student
> Institute of Chemical Biology
> Imperial College London
>
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>
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Received on Thu Oct 14 2010 - 07:00:04 PDT
