AMBER Archive (2006)

Subject: Re: AMBER: how to use AddPdbAtomMap

From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
Date: Thu Aug 24 2006 - 15:27:41 CDT

Dear Seth,

Here is an example for the usage of AddPdbAtomMap:

addPdbAtomMap {
  { 1DH6 DH61 } { 2DH6 DH62 }
  { 1DH2 DH21 } { 2DH2 DH22 }
  { 1DH4 DH41 } { 2DH4 DH42 }
}

In the .pdb file, the name of the atoms are 1DH6, 2DH6, ... By this, leap
will recognize them as DH61, DH62, ... Hope this helps.

Best,

On Thu, 24 Aug 2006 sethl_at_gatech.edu wrote:

> Dear Amber Community,
>
> Could someone please provide an example of how to use AddPdbAtomMap especially
> when dealing with trying to get leap to recognize other types of pdb file
> formats?
>
> If the pdb file of interest is simply not just a 1->1 mapping of different
> names, how would I either convert this file to a leap recognized pdb file or get
> leap to regcognize this?
>
> Thanks,
> Seth Lilavivat
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-- 
  Ilyas Yildirim
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