Dear Dr. Charles I again tried to generate the psf for my pdb of interest using loadPDB. However, this time I get the following comments- PDBTool:read: atom not found in structure: A DG 2 OP1 PDBTool:read: atom not found in structure: B DC 23 OP2 PDBTool:read: atom not found in structure: B DG 24 OP1 PDBTool:read: atom not found in structure: B DG 24 OP2 PDBTool:read: atom not found in structure: B DG 24 HO3' matchInexactAtomEntry: matching entry B 24 OP1 to atom B 24 O1P [rule 4] matchInexactAtomEntry: matching entry B 24 OP2 to atom B 24 O2P [rule 5] matchInexactAtomEntry: matching entry B 24 HO3' to atom B 24 H3T [rule 12] [coords] <protocol.InitCoordsResult instance at 0x104139a28> I cannot find any psf file being written. Is the psf file being generated? Will it be written in the same folder where I have kept all the pdb files? I would really appreciate your help. Thank you so much. Regards Sudakshina Ganguly Senior Research Fellow Department of Biophysics Bose Institute India
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