AMBER Archive (2003)

Subject: Re: pdb_to_mass

From: sychen (yuann_at_bioinfo.ndhu.edu.tw)
Date: Fri Jan 10 2003 - 19:53:37 CST

Hi, Jake,
  try to edit your PDB file, for example,
  ATOM 6 HA ARG 1 1.624 -2.724 -4.154
  ATOM 7 CB ARG 1 3.672 -2.717 -4.839
  ATOM 8 2HB ARG 1 4.638 -2.398 -4.445
  ATOM 9 3HB ARG 1 3.785 -3.735 -5.215
  
  pdb_to_mass script will pick every initial string after ATOM with
  'length=1'. Therefore, sometimes you'll get correct mass returned
  if there is no order number before its name of element, like 'HA' and
  'CB' here, and sometimes you'll get error messages, like '2HB' and
  '3HB'. You can simply edit your pdb file by removing this column and
  try again.
  Good Luck!

sychen

On Fri, 10 Jan 2003 15:42:35 -0500
Jake Isaacs <rjisaa0_at_uky.edu> wrote:
> What is the proper command line syntax for pdb_to_mass? When I enter
> "pdb_to_mass" followed by the pdb filename I get this output (to a file
> if a filename follows the pdb filename):>
> 1.01 16.00 12.00 error in mass parsing 1
> error in mass parsing 2
> 12.00 1.01 16.00 12.00 1.01 14.00 12.00
> 1.01 12.00 1.01 12.00 14.00 1.01 1.01 14.00
> 12.00 16.00