[gmx-users] hdb format of Amber FF ports

[leafyoung81-group at yahoo.com]

Hi, 

If you are using Amber FF ports recently released by
Sorin & Park with Gromacs CVS version, you may
encounter some problems with hdb when using pdb2gmx.

In the changes made after 3.2.1 release, there is one
about the colume in hdb file. Additional colume
describing the name of hydrogen atom is added after
two numbers. To illustrate,

Old (<=3.2.1):
ACE     1
        3       4       CH3     C       O

Current:
ACE     1
        3       4       HH3     CH3     C       O

so I wrote a simple awk script to convert the hdb
files.

BEGIN { }
{
   if ($3!="") {
      if ($3=="N")
         h_name="H"
      else
         h_name=sprintf("H%s", substr($3, 2))
line=sprintf("\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t",
$1,$2, h_name, $3, $4, $5, $6, $7, $8, $9)
      print line
   }
   else
   {
      print $0
   }
}
END { }

Hope this is useful to you.

Yang Ye
Computational Biology Lab
School of Biological Sciences
Nanyang Technological University, Singapore
http://www.ntu.edu.sg/sbs