VMD-L Mailing List

From: Josh Vermaas (vermaas2_at_illinois.edu)
Date: Wed Apr 16 2014 - 14:29:44 CDT

Hi Norge,

Because of how the forcefields are laid out, I don't think there is a
straightforward tool to convert from Amber to Charmm formats. CHAMBER
exists to do the reverse process (dx.doi.org/10.1002/qua.22372), but I
don't think there is much of a market in converting the other way
around, mostly because of how the files are laid out. NAMD cares about
atom-type names when looking up parameters to run simulations, names
that do not directly correspond to those used in Amber. CHARMM is worse,
since it looks up parameters based on atom-type numbers, which
definitely don't correspond to those in Amber. So any such script would
have to writeout the parameters contained in the parmtop file in a
CHARMM-format parameter set. Such a set of parameters wouldn't be
applicable to anything but that exact simulation system (since it would
be missing lots of terms needed in general), leading to a flood of tiny
parameter files to keep track of.

To avoid the need for this, NAMD can use Amber formatted files directly
for input purposes
(http://www.ks.uiuc.edu/Research/namd/2.9/ug/node13.html), and VMD can
load them just fine for visualization and analysis purposes (the Amber
community has a number of minitutorials around, such as at
http://ambermd.org/tutorials/basic/tutorial2/). You could load the
molecule.top and molecule.crd into VMD and write out a fake psf from
there, but it would in no way be suitable to run a simulation and I
really wouldn't recommend it.

-Josh Vermaas

On 04/16/2014 01:24 PM, Norge Cruz Hernández wrote:
>
> Hi,
>
> I am new performing molecular dynamics simulations by using NAMD. I
> have obtained the AMBER format files (molecule.top, molecule.pdb and
> molecule.crd) by using link:
> http://glycam.ccrc.uga.edu/ccrc/carbohydrates/cb_newbuilder.jsp?tool=crystallography&option=ff99:glycam06.
> However, I would like to convert such files to the CHARMM format file
> .psf and .crd or NAMD format file .psf and pdb. Please, could you like
> to recommend me any software ... or script.. to convert (molecule.top
> and molecule.crd) in AMBER format =to=> (molecule.psf and
> molecule.crd) in CHARMM format or (molecule.psf and molecule.pdb) in
> NAMD format?
>
>
>
> Thanks in advance !!!
>
> --
> Prof. Norge Cruz Hernández
> Dpto. Física Aplicada I
> Escuela Técnica Superior de
> Ingeniería Informática
> Universidad de Sevilla
> ave: Reina Mercedes, 41012
> Sevilla, Spain
> Phone number: +34 - 954559970
> Fax number: +34 - 954554341
> http://www.personal.us.es/norge/