[gmx-users] Error of DNA topology

Mark Abraham mark.j.abraham at gmail.com
Tue Jul 11 15:06:29 CEST 2017


Like it says, you'll need to understand why pdb2gmx expects O5' but your
coordinate file doesn't have one. We can't see your files or understand the
context of residue 9.


On Tue, Jul 11, 2017 at 2:14 PM maria khan <mariabiochemist1 at gmail.com>

> 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.
> thanks
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