Subject: 3DNA fiber PDB compatibility with AMBER tleap
Dear AMBER Users,
I am trying to use a DNA structure generated using 3DNA (fiber) as input
for AMBER tleap, but I am encountering fatal errors as:
FATAL: Atom .R<DG5 1>.A<P 32> does not have a type.
FATAL: Atom .R<DG5 1>.A<OP1 33> does not have a type.
FATAL: Atom .R<DG5 1>.A<OP2 34> does not have a type.
FATAL: Atom .R<DC5 17>.A<P 29> does not have a type.
FATAL: Atom .R<DC5 17>.A<OP1 30> does not have a type.
FATAL: Atom .R<DC5 17>.A<OP2 31> does not have a type.
I would appreciate any guidance on the best-practice workflow for
converting 3DNA fiber PDB files into AMBER-compatible input.
Thank you very much for your time and help.
Best regards,
Manvendra Singh
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Received on Thu Jan 08 2026 - 03:00:02 PST
