Hi Marc,
On Tue, Sep 20, 2011 at 5:32 AM, Marc van der Kamp
<marcvanderkamp.gmail.com> wrote:
> I'm trying to analyze a trajectory produced by NAMD with the CHARMM
> force-field, so originally in the .dcd format. I don't have a prmtop for
> this system. Instead, I use a pdb file that I created from the original .psf
> file.
I think I know what's going on here. Ptraj tries to calc the center of
mass of masks containing multiple atoms by default, but the PDB you're
using as your topology file doesn't contain mass. Try running the
calculation with cpptraj; it should automatically detect that there's
no mass info and switch to geometric center for masks with multiple
atoms. Cpptraj doesn't yet support psf/dcd (I'm trying to get it in
there for the next AT release) but will work fine for PDB and amber
coordinates. Let me know if this helps.
-Dan
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Sep 20 2011 - 05:00:03 PDT
