AMBER Archive (2008)

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

From: Balazs JOJART (jojartb_at_pharm.u-szeged.hu)
Date: Fri Jul 18 2008 - 06:09:21 CDT

Hello,
NAMD is able to read directly the prepared amber topology and inpcrd files.
for example:
amber on
parmfile ***.parm7
ambercoor ***.inpcrd or ***.rst
hope this helps.
balazs

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 respectively.
>
> 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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