Hi Dan,
Many thanks for this!
I hadn't thought of this issue - I guess I assumed ptraj would be taking the
geometrical center (instead of center of mass) as well, especially when only
atoms of the same element were selected (which was what I was doing
originally).
Great that cpptraj can do this; I can now get around the issue by making
intermediary .mdcrd files.
Thanks,
Marc
On 20 September 2011 12:37, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> 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
>
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Received on Tue Sep 20 2011 - 07:30:02 PDT
