Thank you very much, Jason.
I have another cpptraj-related question. I'm using this input:
parm rat.parm7
trajin rat.001 remdtraj remdtrajtemp 7.00
autoimage
atominfo :1-2991 out atominfo_7.dat
trajout rat_7.pdb
Why cpptraj is not producing the atominfo_7.dat file? I only have the print
on the screen.
Elisa
On Fri, Sep 2, 2016 at 2:47 AM, Jason Swails <jason.swails.gmail.com> wrote:
> The autoimage command in cpptraj should do that for you.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
>
> > On Sep 1, 2016, at 8:27 AM, Elisa Pieri <elisa.pieri90.gmail.com> wrote:
> >
> > Hi everybody,
> >
> > I performed pH-REMD in explicit solvent, then I reconstructed the
> > "trajectory" for each pH using cpptraj. Due to periodic boundary
> > conditions, my polipeptide is not always centered in the snaphot (i.e. it
> > looks like it is half outside the solvent box). I would like to know if
> it
> > is possible to reorient the vectors and make my polipeptide be in the
> > center of the solvent box, because I need the coordinates and charges for
> > further QM calculations.
> >
> > I hope I have been clear enough!
> > Thanks,
> >
> > Elisa
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Received on Fri Sep 02 2016 - 03:30:02 PDT
