You can create a single residue prmtop from the complex using Parmed.py released with AmberTools.
-Bill
On Dec 10, 2012, at 7:04 AM, "Chandrasekaran, Suryanarayanan" <s.chandrasekaran.jacobs-university.de> wrote:
>
> ________________________________
> From: Chandrasekaran, Suryanarayanan [s.chandrasekaran.jacobs-university.de]
> Sent: Monday, December 10, 2012 1:01 PM
> To: amber.ambermd.org
> Subject:
>
> HI
>
> I need to create .prmtop file for a metal complex residue for bacteriochlorophyll(BCL) complex present in FMO protein, but i got the .prmtop file from another group and they asked us to use protein pdb file insted of .inpcrd file and its working fine for us in "namd", but i need to create .prmtop for the sigle residue BCL. is it possible to extract .prmtop files for a residue from a complete protein .prmtop file. but i dont have .inpcrd insted i have only .pdb file for whole system and for that residue.
>
> otherwise is it possible to create .lib file for that residue from full protein .prmtop file.
>
> thank you
> surya
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Received on Mon Dec 10 2012 - 04:30:03 PST
