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

[Justin A. Lemkul]

P.R.Anand Narayanan wrote:
> 
> 
> ----- 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????
> 

What program did you use to create this new PDB file?  It looks like it severely 
crippled the file, changing just about everything about it.  There is certainly 
no way to use this .pdb file, since there aren't even any residue names defined 
in it.

-Justin

> Please help,
> Thanking you,
> regards,
> Anand
> 
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-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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