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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