AMBER Archive (2006)

Subject: Re: AMBER: protein-ligand interaction

From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
Date: Sat Sep 09 2006 - 16:58:10 CDT

Dear Fenghui,

You should follow the same routines u did with the DNA tutorial. But
before doing this, u need to decide what kind of a simulation u wanna do;
explicit solvent or implicit solvent? If implicit solvent, which method?
Or do u wanna do free energy calculation? U need to decide on these
before starting on creating the prmtop/inpcrd files. After deciding on
that, creating a prmtop/inpcrd files is easy; choose the force field, load
the unknown residue .lib file, load your structure; and after xleap does
not give an error message u create the prmop/inpcrd files. Good luck,

Best,

On Sat, 9 Sep 2006, Fenghui Fan wrote:

> Deal all,
>
> Supposing I get the files of the ligand from
> ANTECHAMBER,and I have the protein-ligand complex PDB
> file. Will you please tell me the commands and the
> command sequence to get and load all the necessary
> files from xleap for sander?
>
> I am looking forward to getting your reply.
>
> Best regards.
>
> Fenghui Fan
>
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-- 
  Ilyas Yildirim
  ---------------------------------------------------------------
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