A small additional tip -- you can see an example of how to use the
"chamber" command in parmed by looking at the relevant tests.
Look at $AMBERHOME/AmberTools/test/parmed/chamber/parmed.in for details.
HTH,
Jason
On Mon, Apr 16, 2018 at 9:06 PM, David A Case <david.case.rutgers.edu>
wrote:
> On Mon, Apr 16, 2018, Ashutosh Shandilya wrote:
> >
> > I am trying to convert psf file (which includes water and ions) to
> convert
> > to prmtop file to have same number of atoms in amber topology as in psf
> > file. I tried the following command in parmed
> >
> > *chamber -top parm99bs0_all.rtf -param par_all36_prot.prm -psf
> ionized.psf
> > -crd ionized.pdb*
> > * -p protein1.prmtop -inpcrd protein1.inpcrd -cmap -verbose*
>
> This doesn't look like the arguments to the chamber action: type "help
> chamber" inside parmed to see the allowable options.
>
> > * UnhandledArgumentWarning: -p protein1.prmtop -inpcrd protein1.inpcrd
> > -cmap -verbose*
>
> As the help page indicates, there are no "-p", "inpcrd", "-cmap" or
> "-verbose" flags. (Are you copying from the now-obsolete stand-alone
> program called chamber?)
>
> You basically use the first two lines above, then use the "parmout"
> action to specify an output prmtop file, and a writeCoordinates action to
> specify an ouptut file for the coordinates.
>
> ...good luck....dac
>
>
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>
--
Jason M. Swails
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Received on Tue Apr 17 2018 - 06:00:04 PDT
