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
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