AMBER Archive (2006)

Subject: Re: AMBER: MD on protein-ligand interaction

From: Ilyas Yildirim (
Date: Thu Sep 14 2006 - 14:09:14 CDT

The coordinates are not important for the simulation if you have prepared
the prmtop/inpcrd files right. I am not sure how Leap is working, but it
will somehow translate the structure to the origin.

You need H-atoms in your prmtop/inpcrd files. When u create the
prmtop/inpcrd files in Leap, it will add those atoms. If there is any
error in Leap, u have to solve those problems.

I will suggest u to do the AMBER tutorials. Good luck.


On Thu, 14 Sep 2006, Fenghui Fan wrote:

> Dear all,
> When we prepare the files for protein-ligand
> interaction MD, supposing we have the original
> protein-ligand complex PDB file, and then we prepare
> the ligand PDB file from the original protein-ligand
> complex PDB file for antechamber, the ligand pdb file
> may contain more atoms (H atoms for example) than the
> original ligand cooordinates in the protein-ligand PDB
> files. Ina adition, the values of the coordinates will
> be significantly different from the values of the
> coordinates, although it still adopt the same
> conformation.
> Should we change the ligand coordinateds in the
> original protein-ligand pdb file to the newly created
> ligand PDB file? Is it necessary? How can we do that?
> I am looking forward to getting your reply.
> Best regards.
> Fenghui Fan
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  Ilyas Yildirim
  - Department of Chemisty       -				-
  - University of Rochester      -				-
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