VMD-L Mailing List

From: Norge Cruz Hernández (norge_at_us.es)
Date: Thu Apr 17 2014 - 10:08:29 CDT

 

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 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 [3]), 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/ [4]). 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 [2]. 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/ [1]
 
Links:
------
[1] http://www.personal.us.es/norge/
[2]
http://glycam.ccrc.uga.edu/ccrc/carbohydrates/cb_newbuilder.jsp?tool=crystallography&option=ff99:glycam06
[3] http://www.ks.uiuc.edu/Research/namd/2.9/ug/node13.html
[4] http://ambermd.org/tutorials/basic/tutorial2/