[gmx-users] Error of DNA topology

maria khan mariabiochemist1 at gmail.com
Tue Jul 11 14:13:41 CEST 2017

Dear gromacs user.

i am simulating protein having DNA ,,when i applied for pdb to gmx
command,it gives me error like  """Residue 9 named DG of a molecule in the
input file was mapped
to an entry in the topology database, but the atom O5' used in
that entry is not found in the input file. Perhaps your atom
and/or residue naming needs to be fixed."""

while using charmm27 all-atom ff.By using gromos 96 43a1 ff, it doesnt form
topology for DNA

kindly give me a detail answer.


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