Hi I have PDB file of DNA (PDB ID: 1D49). I intend generate topology file by pdb2gmx. One error is created: (atom O5 in residue DCYT 1 not found in rtp entry with 21 atom while sorting atom). 2 notes: 1: I checked rtp file for used force field. In rtp file, there is [DCYT] , [DTYM] , [DADE] and [DGUA]. 2: I checked PDB file. residue DCYT 1 has only 16 atoms.
please guide me Mojdeh Akhavan
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