On Tue, Aug 11, 2015 at 4:08 PM, KK R <kkres14.gmail.com> wrote:
> Hi All,
> I am trying to generate Amber topology (prmtop file) from the CHARMM
> generated psf file using 'chamber' program in AmberTools13. I used the
> following command.
>
You could try to change -psf to -xpsf since it's an xplor-style PSF file.
But my more general advice is to upgrade to AmberTools 15 and use the
"chamber" command inside parmed instead. It is more flexible in its
support of various PSF file formats, supports multiple parameter, topology,
and stream files (so you don't have to combine them all), and also
implements NBFIX (which the chamber program never has).
Details for running chamber in ParmEd are in the Amber 15 manual.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Tue Aug 11 2015 - 15:30:05 PDT
