[gmx-users] reg pdb2gmx

[Mark Abraham]

On 10/05/2011 2:31 PM, vidhya sankar wrote:
> Dear justin , Thanks for your valuable previous reply
>
> Also When i run the pdb2gmx tool  i got the following error
>
> WARNING: atom O1 is missing in residue PO4 147 in the pdb file
> WARNING: atom O2 is missing in residue PO4 147 in the pdb file
> WARNING: atom O3 is missing in residue PO4 147 in the pdb file
> WARNING: atom O4 is missing in residue PO4 147 in the pdb file
>
> But my X-ray pdb contains only one united atom as follows
> HETATM 4432  P   PO4 B 147       5.931 -21.573   3.319  1.00 
> 32.97           P
> so it shows errror .
> can i use the -missing topology otherwise
>  Is it better to introduce O atoms in My PDB files ? .if it need How 
> could i introduce new atom or molecule  in My PDB files
>

Build in some oxygen atoms. There are some software suggestions on the 
GROMACS webpage. Try searching around. You may need to rename the atoms 
with a text editor afterwards.

Mark
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