Error: atom C1 not found in buiding block 1MET while combining tdb and rtp

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1

GROMACS version:2023.2-Homebrew
GROMACS modification: Yes/No
Here post your question I need help using charmm36-jul2022.ff I don’t understand why there is a Fatal error:
atom C1 not found in buiding block 1MET while combining tdb and rtp
And I would like to know how to fix it. Thanks.

  gmx pdb2gmx -f model_1.pdb -o model_1.gro -water spc

Select the Force Field:

From current directory:

 1: CHARMM all-atom force field

From '/opt/homebrew/bin/../Cellar/gromacs/2023.2/share/gromacs/top':

 2: AMBER03 protein, nucleic AMBER94 (Duan et al., J. Comp. Chem. 24, 1999-2012, 2003)

 3: AMBER94 force field (Cornell et al., JACS 117, 5179-5197, 1995)

 4: AMBER96 protein, nucleic AMBER94 (Kollman et al., Acc. Chem. Res. 29, 461-469, 1996)

 5: AMBER99 protein, nucleic AMBER94 (Wang et al., J. Comp. Chem. 21, 1049-1074, 2000)

 6: AMBER99SB protein, nucleic AMBER94 (Hornak et al., Proteins 65, 712-725, 2006)

 7: AMBER99SB-ILDN protein, nucleic AMBER94 (Lindorff-Larsen et al., Proteins 78, 1950-58, 2010)

 8: AMBERGS force field (Garcia & Sanbonmatsu, PNAS 99, 2782-2787, 2002)

 9: CHARMM27 all-atom force field (CHARM22 plus CMAP for proteins)

10: GROMOS96 43a1 force field

11: GROMOS96 43a2 force field (improved alkane dihedrals)

12: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)

13: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)

14: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)

15: GROMOS96 54a7 force field (Eur. Biophys. J. (2011), 40,, 843-856, DOI: 10.1007/s00249-011-0700-9)

16: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
1

Using the Charmm36_ljpme-jul2022 force field in directory ./charmm36_ljpme-jul2022.ff

going to rename ./charmm36_ljpme-jul2022.ff/aminoacids.r2b
Opening force field file ./charmm36_ljpme-jul2022.ff/aminoacids.r2b

going to rename ./charmm36_ljpme-jul2022.ff/carb.r2b
Opening force field file ./charmm36_ljpme-jul2022.ff/carb.r2b

going to rename ./charmm36_ljpme-jul2022.ff/cgenff.r2b
Opening force field file ./charmm36_ljpme-jul2022.ff/cgenff.r2b

going to rename ./charmm36_ljpme-jul2022.ff/ethers.r2b
Opening force field file ./charmm36_ljpme-jul2022.ff/ethers.r2b

going to rename ./charmm36_ljpme-jul2022.ff/lipid.r2b
Opening force field file ./charmm36_ljpme-jul2022.ff/lipid.r2b

going to rename ./charmm36_ljpme-jul2022.ff/metals.r2b
Opening force field file ./charmm36_ljpme-jul2022.ff/metals.r2b

going to rename ./charmm36_ljpme-jul2022.ff/na.r2b
Opening force field file ./charmm36_ljpme-jul2022.ff/na.r2b

going to rename ./charmm36_ljpme-jul2022.ff/silicates.r2b
Opening force field file ./charmm36_ljpme-jul2022.ff/silicates.r2b

going to rename ./charmm36_ljpme-jul2022.ff/solvent.r2b
Opening force field file ./charmm36_ljpme-jul2022.ff/solvent.r2b
Reading model_1.pdb...
Read '', 2733 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 285 residues with 2733 atoms

  chain  #res #atoms

  1 'A'   285   2733

All occupancy fields zero. This is probably not an X-Ray structure
All occupancy fields zero. This is probably not an X-Ray structure
Opening force field file ./charmm36_ljpme-jul2022.ff/atomtypes.atp

Reading residue database... (Charmm36_ljpme-jul2022)
Opening force field file ./charmm36_ljpme-jul2022.ff/aminoacids.rtp
Opening force field file ./charmm36_ljpme-jul2022.ff/carb.rtp
Opening force field file ./charmm36_ljpme-jul2022.ff/cgenff.rtp
Opening force field file ./charmm36_ljpme-jul2022.ff/ethers.rtp
Opening force field file ./charmm36_ljpme-jul2022.ff/lipid.rtp
Opening force field file ./charmm36_ljpme-jul2022.ff/metals.rtp
Opening force field file ./charmm36_ljpme-jul2022.ff/na.rtp
Opening force field file ./charmm36_ljpme-jul2022.ff/silicates.rtp
Opening force field file ./charmm36_ljpme-jul2022.ff/solvent.rtp
Opening force field file ./charmm36_ljpme-jul2022.ff/aminoacids.hdb
Opening force field file ./charmm36_ljpme-jul2022.ff/carb.hdb
Opening force field file ./charmm36_ljpme-jul2022.ff/cgenff.hdb
Opening force field file ./charmm36_ljpme-jul2022.ff/ethers.hdb
Opening force field file ./charmm36_ljpme-jul2022.ff/lipid.hdb
Opening force field file ./charmm36_ljpme-jul2022.ff/metals.hdb
Opening force field file ./charmm36_ljpme-jul2022.ff/na.hdb
Opening force field file ./charmm36_ljpme-jul2022.ff/silicates.hdb
Opening force field file ./charmm36_ljpme-jul2022.ff/solvent.hdb
Opening force field file ./charmm36_ljpme-jul2022.ff/aminoacids.n.tdb
Opening force field file ./charmm36_ljpme-jul2022.ff/carb.n.tdb
Opening force field file ./charmm36_ljpme-jul2022.ff/cgenff.n.tdb
Opening force field file ./charmm36_ljpme-jul2022.ff/ethers.n.tdb
Opening force field file ./charmm36_ljpme-jul2022.ff/lipid.n.tdb
Opening force field file ./charmm36_ljpme-jul2022.ff/metals.n.tdb
Opening force field file ./charmm36_ljpme-jul2022.ff/na.n.tdb
Opening force field file ./charmm36_ljpme-jul2022.ff/silicates.n.tdb
Opening force field file ./charmm36_ljpme-jul2022.ff/solvent.n.tdb
Opening force field file ./charmm36_ljpme-jul2022.ff/aminoacids.c.tdb
Opening force field file ./charmm36_ljpme-jul2022.ff/carb.c.tdb
Opening force field file ./charmm36_ljpme-jul2022.ff/cgenff.c.tdb
Opening force field file ./charmm36_ljpme-jul2022.ff/ethers.c.tdb
Opening force field file ./charmm36_ljpme-jul2022.ff/lipid.c.tdb
Opening force field file ./charmm36_ljpme-jul2022.ff/metals.c.tdb
Opening force field file ./charmm36_ljpme-jul2022.ff/na.c.tdb
Opening force field file ./charmm36_ljpme-jul2022.ff/silicates.c.tdb
Opening force field file ./charmm36_ljpme-jul2022.ff/solvent.c.tdb

Back Off! I just backed up topol.top to ./#topol.top.1#

Processing chain 1 'A' (2733 atoms, 285 residues)
Analysing hydrogen-bonding network for automated assignment of histidine
 protonation. 446 donors and 423 acceptors were found.
There are 551 hydrogen bonds
Will use HISE for residue 74
Will use HISE for residue 130
Will use HISE for residue 206
Will use HISE for residue 217
Will use HISE for residue 273
Will use HISE for residue 280
Will use HISE for residue 281
Will use HISE for residue 282
Will use HISE for residue 283
Will use HISE for residue 284
Will use HISE for residue 285

Identified residue MET1 as a starting terminus.

Identified residue HIS285 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Special Atom Distance matrix:
                    MET1   HIS74   CYS79   CYS99  HIS130  MET143  HIS206
                     SD8  NE2725   SG776   SG968 NE21269  SD1384 NE21948
   HIS74  NE2725   4.439
   CYS79   SG776   4.003   1.273
   CYS99   SG968   2.913   1.819   2.177
  HIS130 NE21269   2.580   2.598   1.676   2.207
  MET143  SD1384   2.896   2.781   1.755   2.540   1.044
  HIS206 NE21948   4.319   2.793   3.010   2.571   3.579   3.032
  CYS214  SG2014   4.039   2.000   2.731   1.509   3.343   3.264   1.560
  HIS217 NE22043   5.132   1.515   2.648   2.285   3.836   3.830   2.366
  CYS258  SG2439   1.613   4.149   4.159   2.359   3.268   3.476   3.612
  HIS273 NE22589   3.922   6.072   6.424   4.417   5.621   6.208   6.270
  HIS280 NE22674   5.363   5.140   5.994   4.068   5.934   6.522   5.845
  HIS281 NE22685   5.128   5.063   5.815   4.012   5.641   6.347   6.100
  HIS282 NE22696   5.605   4.880   5.829   3.985   5.941   6.496   5.652
  HIS283 NE22707   6.214   5.512   6.441   4.724   6.522   7.177   6.569
  HIS284 NE22718   6.084   4.870   5.906   4.211   6.186   6.732   5.792
  HIS285 NE22729   6.383   5.688   6.649   4.874   6.755   7.363   6.579
                  CYS214  HIS217  CYS258  HIS273  HIS280  HIS281  HIS282
                  SG2014 NE22043  SG2439 NE22589 NE22674 NE22685 NE22696
  HIS217 NE22043   1.391
  CYS258  SG2439   3.111   4.369
  HIS273 NE22589   5.215   6.143   3.112
  HIS280 NE22674   4.402   4.794   4.221   2.816
  HIS281 NE22685   4.632   4.981   4.224   2.662   0.911
  HIS282 NE22696   4.173   4.424   4.434   3.378   0.613   1.279
  HIS283 NE22707   5.056   5.185   5.186   3.664   1.077   1.201   1.004
  HIS284 NE22718   4.284   4.333   4.934   4.027   1.239   1.732   0.658
  HIS285 NE22729   5.090   5.247   5.264   3.738   1.065   1.487   0.937
                  HIS283  HIS284
                 NE22707 NE22718
  HIS284 NE22718   1.043
  HIS285 NE22729   0.453   0.963
Start terminus MET-1: MET1
End terminus HIS-285: COO-

-------------------------------------------------------
Program:     gmx pdb2gmx, version 2023.2-Homebrew
Source file: src/gromacs/gmxpreprocess/pdb2top.cpp (line 1115)

Fatal error:
atom C1 not found in buiding block 1MET while combining tdb and rtp

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
2

Hi!

Have you tried using the -ter option to choose the proper terminii, as suggested in several other topics?

3

Yes, I have tried using -ter but the result is like this.

Program: gmx pdb2gmx, version 2023.2-Homebrew
Source file: src/gromacs/gmxpreprocess/pdb2gmx.cpp (line 870)

Fatal error:
Atom HG in residue SER 25 was not found in rtp entry SER with 11 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.

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