Fatal error: atom O5' not found in buiding block 1ACE while combining tdb and rtp

User discussions
1

GROMACS version: 2022-2
GROMACS modification: No

Hi,

I’ve tried to perform an MD simulation with a protein-ligand complex. I am using the charmm36-mar2019 force field. When I run “gmx pdb2gmx -f input_clean.pdb -o output_processed.gro” I get the fatal error “atom N not found in buiding block 1ACE while combining tdb and rtp”. Thus, I added the “-ter” and chose 5TER as start and 3TER as end terminus type. However, I get the fatal error “atom O5’ not found in buiding block 1ACE while combining tdb and rtp”. How can I fix it?

Screen output:

going to rename ./charmm36-mar2019.ff/merged.r2b
Opening force field file ./charmm36-mar2019.ff/merged.r2b
Reading pose_clean.pdb…
WARNING: all CONECT records are ignored
Read ‘py109.pdb’, 1854 atoms

Analyzing pdb file
Splitting chemical chains based on TER records or chain id changing.

There are 1 chains and 0 blocks of water and 115 residues with 1854 atoms

chain #res #atoms

1 ’ ’ 115 1854

All occupancies are one
All occupancies are one
Opening force field file ./charmm36-mar2019.ff/atomtypes.atp

Reading residue database… (Charmm36-mar2019)
Opening force field file ./charmm36-mar2019.ff/merged.rtp
Opening force field file ./charmm36-mar2019.ff/merged.hdb
Opening force field file ./charmm36-mar2019.ff/merged.n.tdb
Opening force field file ./charmm36-mar2019.ff/merged.c.tdb

Back Off! I just backed up topol.top to ./#topol.top.9#

Processing chain 1 (1854 atoms, 115 residues)
Analysing hydrogen-bonding network for automated assignment of histidine
protonation. 186 donors and 165 acceptors were found.
There are 259 hydrogen bonds
Will use HISD for residue 13
Will use HISE for residue 48
Will use HISE for residue 59

Identified residue ACE0 as a starting terminus.

Identified residue GLY113 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Special Atom Distance matrix:
HIS13 CYS22 CYS38 HIS48 MET52 CYS55 HIS59
NE2241 SG383 SG624 NE2777 SD825 SG881 NE2930
CYS22 SG383 0.532
CYS38 SG624 1.008 0.642
HIS48 NE2777 1.911 2.072 2.519
MET52 SD825 1.521 1.854 2.146 1.160
CYS55 SG881 1.125 1.534 2.033 1.141 0.859
HIS59 NE2930 1.061 1.557 1.797 2.146 1.251 1.116
MET62 SD989 1.002 1.496 1.835 2.387 1.737 1.269 0.646
MET70 SD1101 0.838 1.292 1.841 1.599 1.332 0.558 1.019
MET62
SD989
MET70 SD1101 0.882
Select start terminus type for ACE-0
0: NH3+
1: NH2
2: 5TER
3: None
2
Start terminus ACE-0: 5TER
Select end terminus type for GLY-113
0: COO-
1: COOH
2: CT2
3: 3TER
4: None
3
End terminus GLY-113: 3TER

Program: gmx pdb2gmx, version 2022.2-spack
Source file: src/gromacs/gmxpreprocess/pdb2top.cpp (line 1132)

Fatal error:
atom O5’ not found in buiding block 1ACE while combining tdb and rtp

For more information and tips for troubleshooting, please check the GROMACS
website at Common Errors — GROMACS webpage https://www.gromacs.org documentation

2

5TER and 3TER are for nucleic acids (5’- and 3’-termini). If you have an N-terminal ACE group, then you need to choose “None” for the terminus patching type and something sensible for the C-terminal GLY (probably COO- in most use cases).

3

If I choose “None” and “COO-” the error below appears:

“Fatal error:
Atom H1 in residue ACE 0 was not found in rtp entry ACE with 6 atoms while sorting atoms.
For a hydrogen, this can be a different protonation state, or it might have had a different number in the PDB file and was rebuilt (it might for instance have been H3, and we only expected H1 & H2). Note that hydrogens might have been added to the entry for the N-terminus. Remove this hydrogen or choose a different protonation state to solve it. Option -ignh will ignore all hydrogens in the input.”

If I add -ignh, the following error shows:
" Fatal error:
Atom CA in residue NMA 113 was not found in rtp entry NMA with 12 atoms
while sorting atoms."

The coordinate file was generated by Glide (Schrodinger Suite) and converted to pdb in ChimeraX. What should I change in the pdb file?

4

Atoms need to be named as specified in the .rtp entries. You need to edit the coordinate file to correct the atom names that are incorrect.