[gmx-users] DNA problem

mojdeh akhavan mojdeh.akhavan at gmail.com
Sat Aug 22 13:08:22 CEST 2009


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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