On Wed, Sep 18, 2013 at 4:11 AM, Chiara Pallara <chiara.pallara.bsc.es>wrote:
> Hi,
> I have some problems to reimage my trajectory using reimage command from
> Amber12 cpptraj. My system contains 2 proteins and one Zn+ ion. I
> managed to center the two proteins but not the Zn+ ion.
>
> I run this command:
> $AMBERHOME/bin/cpptraj start.pdb < reimage.in
> My "reimage.in" file is:
> ------------------------------------
> trajin din1.mdcrd.gz
> trajin din2.mdcrd.gz
> trajout din10ns.mdcrd.gz
>
Replace this:
> center :173-208
> image familiar
> center :173-209
> image familiar
> center :1-209
> image familiar
>
with the following command:
autoimage
If cpptraj complains that 'autoimage' is not a recognized command, make
sure that you have all of the updates applied (and recompile AmberTools 13
if need be).
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Wed Sep 18 2013 - 04:30:03 PDT
