[gmx-users] Fw: Re: Polymer-protein problem

[P.R.Anand Narayanan]

----- Forwarded Message ----
From: P.R.Anand Narayanan <nandu_cooldevil at yahoo.co.in>
To: gromacs <gmx-users at gromacs.org>
Sent: Mon, 18 January, 2010 12:12:45 PM
Subject: Re:Re: Polymer-protein


Dear Gromacs users,

I have to attach a
chemical polymer to a protein and when I created peptide bonds and
saved it, the entire format of the pdb file changed. That is the entire
identity of the protein was lost and the pdb file was saved in the form
of ATOMS and not residues.
That is,
"PROTEIN IN ITS PDB FORMAT"-

ATOM      1  N   GLY
A   3      13.102  19.500  65.823  1.00 35.46           N  
ATOM      2  CA  GLY
A   3      13.351  19.610  64.358  1.00 35.46           C  
ATOM      3  C   GLY
A   3      13.672  18.235  63.779  1.00 35.46           C  
ATOM      4  O   GLY
A   3      12.833  17.341  64.029  1.00 35.46           O  
ATOM      5  N   ILE
A   4      14.789  18.041  63.100  1.00 33.26           N  
ATOM      6  CA  ILE
A   4      15.065  16.703  62.567  1.00 33.26           C  
ATOM      7  C   ILE
A   4      14.891  15.581  63.573  1.00 33.26           C  
ATOM      8  O   ILE
A   4      14.301  14.552  63.227  1.00 33.26           O  
ATOM      9  CB  ILE
A   4      16.488  16.599  61.907  1.00 29.15           C  
ATOM     10  CG1 ILE A   4      16.757  15.146  61.417  1.00 29.15           C  
AFTER BINDING THE POLYMER TO IT, THE PDB IS NOW SAVED AS:
HETATM    1  N           1     -24.998  12.703  12.925
 
HETATM    2  C           2     -24.749  12.813  11.460
HETATM    3  C           3     -24.428  11.438  10.881
HETATM    4  O           4     -25.267  10.544  11.131
HETATM    5  H           5     -25.225  13.528  13.462
HETATM    6  H           6     -25.636  13.216  10.970
HETATM    7  H           7     -23.903  13.478  11.291
HETATM    8  H           8     -24.228  12.218  13.362
HETATM    9  H           9     -25.871  12.195  12.948
HETATM   10  N          10     -23.311  11.244  10.202
    
That is, it is saved as single atoms and not as RESIDUES and hence the entire protein identity is lost. Are there any solutions to this or can I Use the same in gromacs??????? If yes, how can I use it in the pdb2gmx command????

Please help,
Thanking you,
regards,
Anand
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