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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Apr 16 2018 - 18:30:02 PDT
