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On 10/05/2011 2:31 PM, vidhya sankar wrote:
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<td style="font: inherit;" valign="top">Dear justin , Thanks
for your valuable previous reply<br>
<br>
Also When i run the pdb2gmx tool i got the following
error <br>
<br>
WARNING: atom O1 is missing in residue PO4 147 in the pdb
file<br>
WARNING: atom O2 is missing in residue PO4 147 in the pdb
file<br>
WARNING: atom O3 is missing in residue PO4 147 in the pdb
file<br>
WARNING: atom O4 is missing in residue PO4 147 in the pdb
file<br>
<br>
But my X-ray pdb contains only one united atom as follows
<br>
HETATM 4432 P PO4 B 147 5.931 -21.573 3.319
1.00 32.97 P <br>
so it shows errror .<br>
can i use the -missing topology otherwise<br>
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<br>
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<br>
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.<br>
<br>
Mark<br>
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