AMBER Archive (2006)

Subject: Re: AMBER: brookhaven to amber pdb format

From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
Date: Wed Aug 02 2006 - 13:55:38 CDT

You can use the addPdbAtomMap command in leap to make those atoms to be
recognized by leap.

addPdbAtomMap {
  { HG1 HG2 } { HG2 HG3 }
}

Best,

On Wed, 2 Aug 2006, AYTUG TUNCEL wrote:

> Hi all,
>
> Is there any way to convert brookhaven PDB format to AMBER pdb format. Because hydrogen atoms are represented by different nomenclature. for ex:
>
> in MET hydrogens of CG are represented by HG1 and HG2 but in AMBER format they are HG2 and HG3.
>
> thanks for any help
>
> Aytug
>
> -----------------------------------------------------------------------
> 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