On Sat, Apr 25, 2015 at 2:21 PM, sudipta <sudipta.mml.gmail.com> wrote:
> Hi All,
>
> The command line that I use to generate .prmtop and inpcrd is
>
> /home/software/AMBER14/amber14/bin/chamber -top ../top_all27_na.inp -top
> ../top_all22_prot_cmap.inp -param ../par_all27_na.prm -param
> ../par_all22_prot_cmap.inp -xpsf ../KH4_wat_ion.psf -crd ../KH4_wat_ion.pdb
> -p 3jzb_test.prmtop -inpcrd 3jzb_test.inpcrd -cmap
>
> However, it gives the following error
>
> <get_atom_parameters>ERROR atom with mass >1 has type alreadydesignated as
> non-hydrogen type
> <get_atom_parameters> atom 1131 15.999400000000000 O5'
> Cannot continue
>
>
> Please advise me for resolving the issue.
>
> Any help will be appreciated
>
I'm not familiar with this issue. AmberTools 15 (which will be released
in a couple weeks, hopefully), has a completely revamped way of going from
CHARMM PSF and parameter files to Amber topology and coordinate files using
ParmEd instead of the standalone "chamber" program.
You can try downloading ParmEd from Github and trying it out there:
http://github.com/ParmEd/ParmEd
Once you get ParmEd installed, run "parmed.py" and type "help chamber" to
get help on how to use the chamber command (very similar to the chamber
program, with only a small number of differences).
Alternatively, you can wait for a few weeks until AmberTools 15 is
released with a manual that documents exactly how to do it.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Sat Apr 25 2015 - 14:00:11 PDT
