Dear AMBER Community,
I am currently working with FRET probes and modeling a modified nucleotide—TCNitro—in a DNA strand. The issue arises while incorporating this modified residue (UNL, residue 14 in the PDB) and connecting it to the subsequent nucleotide.
Upon inspecting the residue using desc lesionedDNA.14, I observed that the atom naming follows the O3* format (e.g., O3*, C1*, etc.) instead of the standard O3', C1', etc., as shown below:
A<H6 41>
A<C8 40>
A<C7 39>
A<S 38>
A<C14 37>
A<H9 36>
A<C13 35>
A<H8 34>
A<C12 33>
A<O02 32>
A<O01 31>
A<N01 30>
A<C11 29>
A<H7 28>
A<C10 27>
A<C9 26>
A<H 25>
A<N2 24>
A<C6 23>
A<N1 22>
A<O 21>
A<C 20>
A<N 19>
A<H1* 18>
A<C1* 17>
A<O4* 16>
A<H4* 15>
A<H3* 14>
A<H2*2 13>
A<H2*1 12>
A<C2* 11>
A<O3* 10>
A<C3* 9>
A<C4* 8>
A<H5*2 7>
A<H5*1 6>
A<C5* 5>
A<O5* 4>
A<O2P 3>
A<P 2>
A<O1P 1>
As you can see in the pdb instead of having O3' and so on it has O3*.
When I am generating antechamber parameters for this, it works perfectly fine. However when I wish to bond the O3' of the probe to the Phosphorus of the next nucleotide, it is not able to fetch the O3', because of it being named O3*. I also tried fetching O3* but it just raises the error:
bond lesionedDNA.14.O3* lesionedDNA.15.P
Error: bond: Argument #1 is of type String must be of type: [atom]
Here are some suggestions for correcting this error:
Verify the type of an argument with the desc command.
Check for alternate argument names with the list command.
usage: bond <atom1> <atom2> [order]
Naturally the first solution that comes to our mind is to manually change the * to ' . I did that and generated the antechamber files(prepi,frcmod and lib files) and using the lib files and frcmod for tleap.
However I get the set of errors:
FATAL: Atom .R<UNL 14>.A<N 1> does not have a type.
FATAL: Atom .R<UNL 14>.A<C 2> does not have a type.
FATAL: Atom .R<UNL 14>.A<O 3> does not have a type.
FATAL: Atom .R<UNL 14>.A<P 4> does not have a type.
FATAL: Atom .R<UNL 14>.A<O1P 5> does not have a type.
FATAL: Atom .R<UNL 14>.A<O2P 6> does not have a type.
FATAL: Atom .R<UNL 14>.A<C5' 7> does not have a type.
FATAL: Atom .R<UNL 14>.A<O5' 8> does not have a type.
FATAL: Atom .R<UNL 14>.A<C4' 9> does not have a type.
FATAL: Atom .R<UNL 14>.A<O4' 10> does not have a type.
FATAL: Atom .R<UNL 14>.A<C3' 11> does not have a type.
FATAL: Atom .R<UNL 14>.A<O3' 12> does not have a type.
FATAL: Atom .R<UNL 14>.A<C2' 13> does not have a type.
FATAL: Atom .R<UNL 14>.A<C1' 14> does not have a type.
FATAL: Atom .R<UNL 14>.A<N01 15> does not have a type.
FATAL: Atom .R<UNL 14>.A<N1 16> does not have a type.
FATAL: Atom .R<UNL 14>.A<O01 17> does not have a type.
FATAL: Atom .R<UNL 14>.A<N2 18> does not have a type.
FATAL: Atom .R<UNL 14>.A<O02 19> does not have a type.
FATAL: Atom .R<UNL 14>.A<C6 20> does not have a type.
FATAL: Atom .R<UNL 14>.A<C7 21> does not have a type.
FATAL: Atom .R<UNL 14>.A<C8 22> does not have a type.
FATAL: Atom .R<UNL 14>.A<C9 23> does not have a type.
FATAL: Atom .R<UNL 14>.A<C10 24> does not have a type.
FATAL: Atom .R<UNL 14>.A<C11 25> does not have a type.
FATAL: Atom .R<UNL 14>.A<C12 26> does not have a type.
FATAL: Atom .R<UNL 14>.A<C13 27> does not have a type.
FATAL: Atom .R<UNL 14>.A<C14 28> does not have a type.
FATAL: Atom .R<UNL 14>.A<S 29> does not have a type.
FATAL: Atom .R<UNL 14>.A<H 30> does not have a type.
FATAL: Atom .R<UNL 14>.A<H6 31> does not have a type.
FATAL: Atom .R<UNL 14>.A<H7 32> does not have a type.
FATAL: Atom .R<UNL 14>.A<H8 33> does not have a type.
FATAL: Atom .R<UNL 14>.A<H9 34> does not have a type.
FATAL: Atom .R<UNL 14>.A<H1' 35> does not have a type.
FATAL: Atom .R<UNL 14>.A<H3' 36> does not have a type.
FATAL: Atom .R<UNL 14>.A<H4' 37> does not have a type.
FATAL: Atom .R<UNL 14>.A<H2'1 38> does not have a type.
FATAL: Atom .R<UNL 14>.A<H2'2 39> does not have a type.
FATAL: Atom .R<UNL 14>.A<H5'1 40> does not have a type.
FATAL: Atom .R<UNL 14>.A<H5'2 41> does not have a type.
/home/rahul/miniconda3/envs/AmberTools23/bin/teLeap: Fatal Error!
This suggests that the atom types are not being recognized after renaming, despite the presence of a proper .prepi and .frcmod.
It seems like a minor naming issue is preventing the correct setup of the structure. I would appreciate any guidance on how to properly handle this—particularly how to:
*
Bond residues with non-standard atom names like O3*, or
*
Safely rename atoms to standard names (O3') without breaking the atom typing and library generation.
Thank you very much in advance for your help!
Best regards,
Rahul Singal
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Received on Thu Apr 17 2025 - 03:30:03 PDT
