On Thu, Jan 08, 2026, MANVENDRA SINGH via AMBER wrote:
>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.
The 3DNA code is adding a 5' phosphate group to the end of each chain. The
default in Amber is to not have such a group. You could choose two options:
1. remove the PO2 group from the 5' end of each chain;
2. load the "terminal_monophosphate.lib" library in tleap before you issue
the loadPdb command. This will tell Amber to do what 3DNA is expecting.
Option 1 is usually more appropriate if you are working with synthetic DNA,
where option 2 may better reflect a fragment of DNA extracted from a longer
sequence.
...good luck...dac
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Received on Thu Jan 08 2026 - 21:00:03 PST
