[gmx-users] reg pdb2gmx
Mark.Abraham at anu.edu.au
Tue May 10 11:29:13 CEST 2011
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.
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