PDB files from 3DNA and AMBER compatibility

[sravi]

Hello Moderator and other Users:

I am interested in using the dsDNA (PDB file) created by X3DNA to do some AMBER simulations.

After starting a tleap session (amber14). I am reading the "s0.pdb" created using X3DNA.
The s0.pdb was created using Generic BDNA template for "ATATATATAT". When I run tleap, I get the
following errors (shown below) and I think this is coming from either atom name or PDB format mismatch. Does anyone have any
experience in using the DNA PDB file created by X3DNA in AMBER (tleap etc.)? 

Thanks

Ravi

dna1 = loadpdb "s0.pdb" 
> check dna1
Checking 'dna1'....
ERROR: The unperturbed charge of the unit: -8.616200 is not integral.
WARNING: The unperturbed charge of the unit: -8.616200 is not zero.
FATAL:  Atom .R<A5 1>.A<P 32> does not have a type.
FATAL:  Atom .R<A5 1>.A<O1P 33> does not have a type.
FATAL:  Atom .R<A5 1>.A<O2P 34> does not have a type.
FATAL:  Atom .R<T 2>.A<P 1> does not have a type.
FATAL:  Atom .R<T 2>.A<O1P 2> does not have a type.
FATAL:  Atom .R<T 2>.A<O2P 3> does not have a type.
FATAL:  Atom .R<T 2>.A<O5' 4> does not have a type.
FATAL:  Atom .R<T 2>.A<C5' 5> does not have a type.
FATAL:  Atom .R<T 2>.A<C4' 6> does not have a type.
FATAL:  Atom .R<T 2>.A<O4' 7> does not have a type.
FATAL:  Atom .R<T 2>.A<C3' 8> does not have a type.
FATAL:  Atom .R<T 2>.A<O3' 9> does not have a type.
FATAL:  Atom .R<T 2>.A<C2' 10> does not have a type.
......Truncated

[xiangjun]

Hi Ravi,

3DNA fiber models follow PDB v3, using DA/DT/GC/DG for DNA nucleotides, OP1/OP2 instead of O1P/O2P, C7 instead of C5M for DT, C1' instead of C1* etc for sugar atoms as in PDB v2. AMBER tleap may prefer a customized PDB variant. To verify, you could download a B-DNA PDB structure (e.g., 1bna) to see how AMBER responds.

I believe what you encountered is a common AMBER question, and you'll most likely get a resolution from the AMBER mailing list.

Best regards,

Xiang-Jun