VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Thu Apr 17 2014 - 11:03:49 CDT

On Thu, Apr 17, 2014 at 11:08 AM, Norge Cruz Hernández <norge_at_us.es> wrote:
> Hi Josh,
>
> I can perform molecular dynamics simulations by using the files molecule.top
> and molecule.crd. i.e., input in AMBER file format. So, I can perform it by
> using " amber on", "parmfile molecule.top" and "ambercoor 4_gg.crd". It
> worked.
>
> However, I need to perform molecular dynamics simulations in a system
> "A+molecule", but the input files for subsystem A are A.pdb and A.psf, i.e.,
> file format to be used by NAMD. So, I was thinking the way to convert
> molecule.top and molecule.crd >=to=> molecule.psf and molecule.pdb, and put
> it all together by using "Merge Structures" in vmd. I know, that it is
> possible to get the molecule.pdb file from molecule.crd and molecule.top.
> However, I was not able to get the .psf file comming from this pdb file.

that would be useless, since in addition to a .psf (=topology) and a
.pdb (=coordinates) file, you also need the parameters. as has been
pointed out, there is no clean conversion from amber parameters to the
CHARMM format. better you stick to amber and use the tools provided
with amber to merge your structures.

axel.

>
> That is the point ... can you help me ...
>
> Thanks !!!
>
> ---
>
> 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/
>
> El 16/04/2014 21:29, Josh Vermaas escribió:
>
> 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/ 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.