Re: how to generate psf file using the AMBER topology file

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Fri Jul 18 2008 - 15:30:45 CDT

Hi Madhurima,
you have two choices for this: You can either find a charmm-formatted
version of the amber topologies (some of these are bundled with the
charmm forcefield distributions -- see
http://mackerell.umaryland.edu/CHARMM_ff_params.html), or you can make
amber coor/parm files in [xt]leap and then run simulations in namd
directly on these files (see
http://www.ks.uiuc.edu/Research/namd/2.6/ug/node15.html for instructions).
Best,
Peter

tinni sona wrote:
> Hi All,
>
> I want to perform the MD simulation of protein-carbohydrate complex
> using NAMD. My force field is AMBER. I'm failed to generate the
> required psf file for the system using the AMBER and GLYCAM topology
> files for protein and carbohydrate. However using CHARMM topology file
> for protein the psf file for protein is generating nicely.
>
> Can anyone please suggest me how to generate the psf file using
> topology file taken from AMBER?
> I would really appreciate if you could respond.
>
> Thanks,
> Madhurima

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