Help on how to solve "atom N not found in building block 1ADE while combining tdb and rtp"

User discussions
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GROMACS version: 2020.1
GROMACS modification: Yes/No

Dear Gromacs users,

I downloaded the last version of the CHARMM36 ff from the MacKerell lab website and I intended to use this ff with pdb2gmx to obtain the topology of a pdb file that I have for a RNA sequence.

When running pdb2gmx it shows me the following error:
"atom N not found in building block 1ADE while combining tdb and rtp"

Now when checking the rtp for the FF I realized that there are not definition for 3’- and 5’-terminal nucleotides of a RNA sequence, or at least I can not find them. So it seems to me that the FF does not recognize the 1ADE (5’-adenosine) and the same will happen for the 3’-teminal CYT140. So the program can not find P or O1P or O2P, but this is my guess.
How could I correct this problem? Is there any way to add the 5- and 3’-terminal nucleotides to the .rtp file of the FF, or if they are there how to located them? What would be the name of these nucleotides in the rtp for CHARMM36?

As alternative solution I also generated the Gromacs compatible CHARMM36 topologies for this pdb using CHARMM-GUI. Is this a good enough solution?

Would appreciate any help with this.

Kindly,
Lazaro

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You have to interactively select the appropriate terminal patches (5TER and 3TER), otherwise the first ones in the list (NTER and CTER, for proteins) get applied and pdb2gmx chokes on the missing atoms (which rightly shouldn’t be there).

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Dear Dr. Jalemkul,

Thanks for the quick reply.

Do you refer with select the appropriately terminal patches to change the name of the atoms in my pdb to 5TER for example? I tried that and still get the same message.

Kindly,
Lazaro

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Don’t change atom names. Select the appropriate patches (5TER and 3TER) when prompted by pdb2gmx.

1 Like
5

Thank you very much Dr Jalemkul. I used -ter option for pdb2gmx and choosed 5TER and 3TER and it worked.

Thanks again

6

Atom OP1 in residue A 1 was not found in rtp entry ADE with 31 atoms
while sorting atoms.
.
I did the same steps , but it did not work for me in charmm 36ff . Please help

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CHARMM uses O1P and O2P for non-bridging phosphate oxygens, not OP1 and OP2, so you need to fix those in your input coordinate file.

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I am getting the same error after following this discussion. Did the bug resolve?
I am using charmm-july2021.ff for 1bna.pdb. I have 2 chains with 12-residue each. @awacha , the terminal patching seems to be an error when I use -ter option of gromacs with None after it. 5’-ter residue name and 3’-ter residue name i have changed and also in na.rtp file. (ex-DCS for 5’-cytosine and DGE for 3’-ter guanine). How ever i am still getting error that i have attached the screen shot. It is not picking the first residue as starting terminal.
Back Off! I just backed up topol.top to ./#topol.top.11#

Processing chain 1 (379 atoms, 12 residues)

Warning: Starting residue DSC1 in chain not identified as Protein/RNA/DNA.

This chain lacks identifiers, which makes it impossible to do strict

classification of the start/end residues. Here we need to guess this residue

should not be part of the chain and instead introduce a break, but that will

be catastrophic if they should in fact be linked. Please check your structure,

and add DSC to residuetypes.dat if this was not correct.

Identified residue DG2 as a starting terminus.

Warning: Residue DGE12 in chain has different type (‘Other’) from

residue DG2 (‘DNA’). This chain lacks identifiers, which makes

it impossible to do strict classification of the start/end residues. Here we

need to guess this residue should not be part of the chain and instead

introduce a break, but that will be catastrophic if they should in fact be

linked. Please check your structure, and add DGE to residuetypes.dat

if this was not correct.

Identified residue DC11 as a ending terminus.

8 out of 8 lines of specbond.dat converted successfully

Select start terminus type for DG-2

0: NH3+

1: NH2

2: 5MET

3: 5PHO

4: 5POM

5: 5TER

6: None

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Start terminus DG-2: None

Select end terminus type for DC-11

0: COO-

1: COOH

2: CT1

3: CT2

4: 3TER

5: None

5

End terminus DC-11: None

Program: gmx pdb2gmx, version 2019

Source file: src/gromacs/gmxpreprocess/pdb2top.cpp (line 1075)

Fatal error:

There is a dangling bond at at least one of the terminal ends. Fix your

coordinate file, add a new terminal database entry (.tdb), or select the

proper existing terminal entry.

For more information and tips for troubleshooting, please check the GROMACS

website at Common Errors — GROMACS webpage https://www.gromacs.org documentation

application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0

[unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=1

:

system msg for write_line failure : Bad file descriptor

Screenshot 2022-08-15 at 9.14.54 AM
Screenshot 2022-08-15 at 9.14.54 AM1672×1678 151 KB

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please provide me by the command that you have been used .
I tried -ter option & the feedback Unknown command-line option -ter option

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gmx pdb2gmx -f input.gro -ter will be ok.