On Wed, Feb 20, 2013, Asmita Gupta wrote:
>
> I am trying to randomize the positions of Na and Cl ions around the
> solute using both ptraj and cpptraj. However, the restart file generated by
> ptraj has box information in it, whereas cpptraj is not writing any box
> information to the restart file generated using trajout.. What could be the
> reason behind this behaviour?
>
> these are the command used :
>
> trajin ternary.pdb
This is your problem: pdb files don't have any box information in them. There
is box information in the prmtop file, but cpptraj can't be sure that the
prmtop info is correct (since the box size is a dynamical variable). Best
thing is to use a restart file as input if you want a restart file as output.
...good luck....dac
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Received on Wed Feb 20 2013 - 05:00:05 PST
