AMBER Archive (2006)

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

From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
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.

Best,

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
>
> __________________________________________________
> Do You Yahoo!?
> Tired of spam? Yahoo! Mail has the best spam protection around
> http://mail.yahoo.com
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
>
>

-- 
  Ilyas Yildirim
  ---------------------------------------------------------------
  - Department of Chemisty       -				-
  - University of Rochester      -				-
  - Hutchison Hall, # B10        -				-
  - Rochester, NY 14627-0216     - Ph.:(585) 275 67 66 (Office)	-
  - http://www.pas.rochester.edu/~yildirim/			-
  ---------------------------------------------------------------

----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to amber_at_scripps.edu To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu