Hi,
A message like:
> FATAL: Atom .R<UNL 14>.A<N 1> does not have a type.
means that Leap doesn't have enough information to know what to do
with the atom named N in residue template UNL. You need to go back
through your lib file and make sure that:
1) The residue template contains all atoms, and the atoms are all
named whatever they are in your input PDB/mol2.
2) The atoms all have an atom type.
3) The parameters you load (standard force field files like GAFF plus
your additional parameters) contain all necessary parameters for those
atom types. For example, if your atom type for N is NX, and it is
bonded to an atom named C with type CX, there had better be a bond
parameter for NX-CX somewhere in your parameter set.
Again, leap is just a bookkeeping program and only knows what you tell
it. You need to make sure it has all the information. Try isolating
your custom residue (i.e. create a PDB with just UNL) and see if you
can just build that; it should make debugging easier.
-Dan
On Thu, Apr 17, 2025 at 9:27 AM Rahul Singal
<rahul.singal.research.iiit.ac.in> wrote:
>
> Hi There,
> Thank you for your response.
> I believe there may have been a misunderstanding regarding the issue I'm facing. I have successfully generated the frcmod and lib files for the probe without any errors. However, in the PDB file, the atom is labeled as O3*, as mentioned in my previous email. When I attempt to create a bond using the following command:
> bond lesionedDNA.14.O3* lesionedDNA.15.P
>
> I receive the following error message:
>
> 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]
>
> To troubleshoot, I modified the PDB file and replaced O3* with O3' (and made similar changes for other atoms). However, this results in a fatal error, despite regenerating the frcmod and lib files accordingly. I have ensured that the issue is not due to any fault on my part during this process.
> Could you please advise on how to resolve this formatting issue and ensure correct atom recognition for bond creation?
> Looking forward to your guidance.
> Best regards,
> Rahul Singal
>
>
> ________________________________
> From: Daniel Roe <daniel.r.roe.gmail.com>
> Sent: Thursday, April 17, 2025 6:17 PM
> To: Rahul Singal <rahul.singal.research.iiit.ac.in>; AMBER Mailing List <amber.ambermd.org>
> Subject: Re: [AMBER] Assistance Required with Custom Residue Bonding and Atom Naming in TCNitro Structure
>
> Hi,
>
> Leap is just a bookkeeping program at heart. You need to load a
> template (a .lib or .prepin file) so that it knows what atom
> names/types/connectivity to expect for the UNL residue, i.e. before
> you load a structure with residue UNL you'll need to do something
> like:
>
> loadoff UNL.lib
> loadamberparams UNL.frcmod
>
> where UNL.frcmod contains whatever parameters are needed for your
> custom residue (generated with e.g. parmchk2).
>
> See the following tutorials on generating custom residues to get more
> information:
> https://ambermd.org/tutorials/basic/tutorial5/index.php
> https://carlosramosg.com/amber-custom-residue-parameterization
>
> Good luck!
>
> -Dan
>
> On Thu, Apr 17, 2025 at 6:03 AM Rahul Singal via AMBER
> <amber.ambermd.org> wrote:
> >
> > 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
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
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Received on Thu Apr 17 2025 - 07:00:02 PDT
