Hi Dan,
Thanks for the answers. The ptraj was for some reason reading the charge
for the atom types having characters
greater than 4, something charmm has now incorporated with ioformat exten.
I used psfgen to generate
a charmm psf and it seems to read the masses correctly.
The mwcovar seems to make sense.
However, the displ.dat and fluct.dat still seems to give me 0.00.. need
to debug more.
I can send you the psf and dcd files. Will do that tomorrow.
Not tried cpptraj. Have not used that before.
thanks,
ganesh
On Mon, Sep 17, 2012 at 5:53 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> On Monday, September 17, 2012, Ganesh Kamath wrote:
> >
> > I also get a bunch of NAN in the mwcovar.dat matrix. However covariance
> > matrix, distance matrix and correl
> > are generated correctly.
>
>
> This indicates that for some reason the masses are not being read in
> correctly from your psf file. Have you tried cpptraj? Do you get the same
> result?
>
> Please send me off-list your psf and 1 or 2 frames of your dcd so I can try
> to reproduce the error. Thanks!
>
> -Dan
>
>
> >
> > Can anyone please help.
> >
> > thanks,
> > ganesh
> > _______________________________________________
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>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 201
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
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Received on Mon Sep 17 2012 - 17:30:03 PDT
