Atom not in the rtp entry reported not to be found in the input file

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GROMACS version: 2019.3
GROMACS modification: Yes/No
Here post your question

Hello everyone.

I’m having some trouble running pdb2gmx command using AMBER99SB forcefield.

I am trying to simulate a PNA molecule, so I added the PNA residue information in the aminoacids.rtp, aminoacids.hdb, and aminoacids.r2b file.

I also added the residue names in the residuetype.dat, but when I run pdb2gmx, I get this error:

going to rename amber99sb-PNA.ff/aminoacids.r2b
Opening force field file /opt/gromacs/2019.3/share/gromacs/top/amber99sb-PNA.ff/aminoacids.r2b
going to rename amber99sb-PNA.ff/dna.r2b
Opening force field file /opt/gromacs/2019.3/share/gromacs/top/amber99sb-PNA.ff/dna.r2b
going to rename amber99sb-PNA.ff/rna.r2b
Opening force field file /opt/gromacs/2019.3/share/gromacs/top/amber99sb-PNA.ff/rna.r2b
Reading 1pdt_model1_New.pdb…
Read ‘’, 317 atoms
Renaming atom ‘O2’ in residue 16 PC to ‘OXT’
Analyzing pdb file
Splitting chemical chains based on TER records or chain id changing.
There are 2 chains and 0 blocks of water and 16 residues with 317 atoms

chain #res #atoms
1 ‘A’ 8 162
2 ‘B’ 8 155

All occupancies are one
Opening force field file /opt/gromacs/2019.3/share/gromacs/top/amber99sb-PNA.ff/atomtypes.atp
Atomtype 67
Reading residue database… (Amber99sb-PNA)
Opening force field file /opt/gromacs/2019.3/share/gromacs/top/amber99sb-PNA.ff/aminoacids.rtp
Residue 109
Sorting it all out…
Opening force field file /opt/gromacs/2019.3/share/gromacs/top/amber99sb-PNA.ff/dna.rtp
Residue 125
Sorting it all out…
Opening force field file /opt/gromacs/2019.3/share/gromacs/top/amber99sb-PNA.ff/rna.rtp
Residue 141
Sorting it all out…
Opening force field file /opt/gromacs/2019.3/share/gromacs/top/amber99sb-PNA.ff/aminoacids.hdb
Opening force field file /opt/gromacs/2019.3/share/gromacs/top/amber99sb-PNA.ff/dna.hdb
Opening force field file /opt/gromacs/2019.3/share/gromacs/top/amber99sb-PNA.ff/rna.hdb
Opening force field file /opt/gromacs/2019.3/share/gromacs/top/amber99sb-PNA.ff/aminoacids.n.tdb
Opening force field file /opt/gromacs/2019.3/share/gromacs/top/amber99sb-PNA.ff/aminoacids.c.tdb

Processing chain 1 ‘A’ (162 atoms, 8 residues)
Identified residue DG1 as a starting terminus.
Identified residue DC8 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Changing rtp entry of residue 1 DG to ‘DG5’
Changing rtp entry of residue 8 DC to ‘DC3’
Opening force field file /opt/gromacs/2019.3/share/gromacs/top/amber99sb-PNA.ff/aminoacids.arn
Opening force field file /opt/gromacs/2019.3/share/gromacs/top/amber99sb-PNA.ff/dna.arn
Opening force field file /opt/gromacs/2019.3/share/gromacs/top/amber99sb-PNA.ff/rna.arn
Renaming atom ‘OP1’ in residue 2 DA to ‘O1P’
Renaming atom ‘OP2’ in residue 2 DA to ‘O2P’
Renaming atom ‘OP1’ in residue 3 DC to ‘O1P’
Renaming atom ‘OP2’ in residue 3 DC to ‘O2P’
Renaming atom ‘OP1’ in residue 4 DA to ‘O1P’
Renaming atom ‘OP2’ in residue 4 DA to ‘O2P’
Renaming atom ‘OP1’ in residue 5 DT to ‘O1P’
Renaming atom ‘OP2’ in residue 5 DT to ‘O2P’
Renaming atom ‘OP1’ in residue 6 DA to ‘O1P’
Renaming atom ‘OP2’ in residue 6 DA to ‘O2P’
Renaming atom ‘OP1’ in residue 7 DG to ‘O1P’
Renaming atom ‘OP2’ in residue 7 DG to ‘O2P’
Renaming atom ‘OP1’ in residue 8 DC to ‘O1P’
Renaming atom ‘OP2’ in residue 8 DC to ‘O2P’
Checking for duplicate atoms…
Generating any missing hydrogen atoms and/or adding termini.
Now there are 8 residues with 253 atoms
Chain time…

Making bonds…
Number of bonds was 273, now 273
Generating angles, dihedrals and pairs…
Before cleaning: 655 pairs
Before cleaning: 720 dihedrals
Keeping all generated dihedrals
Making cmap torsions…
There are 720 dihedrals, 45 impropers, 492 angles
631 pairs, 273 bonds and 0 virtual sites
Total mass 2411.628 a.m.u.
Total charge -7.000 e
Writing topology

Processing chain 2 ‘B’ (155 atoms, 8 residues)
Identified residue PG9 as a starting terminus.
Identified residue PC16 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Changing rtp entry of residue 9 PG to ‘NPG’
Changing rtp entry of residue 16 PC to ‘CPC’
Opening force field file /opt/gromacs/2019.3/share/gromacs/top/amber99sb-PNA.ff/aminoacids.arn
Opening force field file /opt/gromacs/2019.3/share/gromacs/top/amber99sb-PNA.ff/dna.arn
Opening force field file /opt/gromacs/2019.3/share/gromacs/top/amber99sb-PNA.ff/rna.arn
Checking for duplicate atoms…
Generating any missing hydrogen atoms and/or adding termini.

Program: gmx pdb2gmx, version 2019.3
Source file: src/gromacs/gmxpreprocess/pgutil.cpp (line 128)

Fatal error:
Residue 2 named PC of a molecule in the input file was mapped
to an entry in the topology database, but the atom N9 used in
that entry is not found in the input file. Perhaps your atom
and/or residue naming needs to be fixed.

But what’s interesting is, there is NO N9 atom in the pdb or in the rtp file!

PDB:

ATOM 255 C8’ PG B 9 -6.073 14.982 -5.593 1.00 0.71 C
ATOM 256 C7’ PG B 9 -7.271 14.394 -6.343 1.00 0.66 C
ATOM 257 O7’ PG B 9 -7.571 13.227 -6.178 1.00 0.65 O
ATOM 258 C5’ PG B 9 -9.096 14.543 -7.965 1.00 0.79 C
ATOM 259 C’ PG B 9 -8.792 13.313 -8.828 1.00 0.73 C
ATOM 260 O1’ PG B 9 -8.550 13.427 -10.014 1.00 0.81 O
ATOM 261 N4’ PG B 9 -7.965 15.142 -7.183 1.00 0.73 N
ATOM 262 C3’ PG B 9 -7.632 16.591 -7.364 1.00 0.85 C
ATOM 263 C2’ PG B 9 -8.303 17.417 -6.266 1.00 0.93 C
ATOM 264 N1’ PG B 9 -9.401 16.943 -5.740 1.00 1.35 N
ATOM 265 N9 PG B 9 -5.227 14.067 -4.794 1.00 0.70 N
ATOM 266 C8 PG B 9 -5.437 13.568 -3.541 1.00 0.74 C
ATOM 267 N7 PG B 9 -4.463 12.848 -3.064 1.00 0.75 N
ATOM 268 C5 PG B 9 -3.521 12.864 -4.092 1.00 0.67 C
ATOM 269 C6 PG B 9 -2.238 12.255 -4.165 1.00 0.66 C
ATOM 270 O6 PG B 9 -1.657 11.583 -3.316 1.00 0.75 O
ATOM 271 N1 PG B 9 -1.618 12.525 -5.373 1.00 0.60 N
ATOM 272 C2 PG B 9 -2.160 13.272 -6.394 1.00 0.62 C
ATOM 273 N2 PG B 9 -1.421 13.394 -7.491 1.00 0.66 N
ATOM 274 N3 PG B 9 -3.361 13.846 -6.334 1.00 0.65 N
ATOM 275 C4 PG B 9 -3.984 13.604 -5.158 1.00 0.65 C
ATOM 276 H1 PG B 9 -0.672 12.182 -5.468 1.00 0.59 H
ATOM 277 H8’1 PG B 9 -6.445 15.760 -4.927 1.00 0.81 H
ATOM 278 H8’2 PG B 9 -5.426 15.454 -6.332 1.00 0.76 H
ATOM 279 H5’1 PG B 9 -9.883 14.271 -7.262 1.00 0.84 H
ATOM 280 H5’2 PG B 9 -9.489 15.316 -8.624 1.00 0.90 H
ATOM 281 H3’1 PG B 9 -6.552 16.731 -7.308 1.00 0.88 H
ATOM 282 H3’2 PG B 9 -7.991 16.929 -8.335 1.00 0.96 H
ATOM 283 H2’1 PG B 9 -7.543 17.788 -5.580 1.00 1.05 H
ATOM 284 H2’2 PG B 9 -8.825 18.260 -6.719 1.00 1.09 H
ATOM 285 H1’1 PG B 9 -9.706 16.009 -5.974 1.00 1.55 H
ATOM 286 H1’2 PG B 9 -9.879 17.462 -5.018 1.00 1.73 H
ATOM 287 H8 PG B 9 -6.351 13.762 -2.981 1.00 0.80 H
ATOM 288 HN21 PG B 9 -0.495 12.992 -7.523 1.00 0.54 H
ATOM 289 HN22 PG B 9 -1.787 13.889 -8.292 1.00 0.93 H
ATOM 290 C8’ PC B 10 -5.210 10.413 -8.000 1.00 0.48 C
ATOM 291 C7’ PC B 10 -5.583 9.462 -9.149 1.00 0.50 C
ATOM 292 O7’ PC B 10 -5.021 8.392 -9.255 1.00 0.52 O
ATOM 293 C5’ PC B 10 -6.823 8.890 -11.181 1.00 0.57 C
ATOM 294 C’ PC B 10 -5.674 8.373 -12.060 1.00 0.55 C
ATOM 295 O1’ PC B 10 -5.862 7.463 -12.844 1.00 0.62 O
ATOM 296 N4’ PC B 10 -6.504 9.803 -10.030 1.00 0.54 N
ATOM 297 C3’ PC B 10 -7.242 11.096 -9.896 1.00 0.59 C
ATOM 298 C2’ PC B 10 -8.474 10.882 -9.007 1.00 0.63 C
ATOM 299 N1’ PC B 10 -8.803 12.134 -8.247 1.00 0.67 N
ATOM 300 N1 PC B 10 -4.743 9.831 -6.726 1.00 0.47 N
ATOM 301 C2 PC B 10 -3.369 9.916 -6.413 1.00 0.43 C
ATOM 302 N3 PC B 10 -2.947 9.399 -5.217 1.00 0.43 N
ATOM 303 C4 PC B 10 -3.817 8.818 -4.382 1.00 0.44 C
ATOM 304 C5 PC B 10 -5.209 8.714 -4.715 1.00 0.50 C
ATOM 305 C6 PC B 10 -5.619 9.236 -5.883 1.00 0.53 C
ATOM 306 O2 PC B 10 -2.556 10.391 -7.223 1.00 0.47 O
ATOM 307 N4 PC B 10 -3.382 8.364 -3.206 1.00 0.49 N
ATOM 308 H8’1 PC B 10 -6.086 11.022 -7.777 1.00 0.52 H
ATOM 309 H8’2 PC B 10 -4.426 11.077 -8.365 1.00 0.48 H
ATOM 310 H5’1 PC B 10 -7.519 9.417 -11.835 1.00 0.63 H
ATOM 311 H5’2 PC B 10 -7.341 8.021 -10.778 1.00 0.62 H
ATOM 312 H3’1 PC B 10 -6.593 11.850 -9.450 1.00 0.56 H
ATOM 313 H3’2 PC B 10 -7.562 11.436 -10.881 1.00 0.65 H
ATOM 314 H2’1 PC B 10 -9.325 10.602 -9.628 1.00 0.68 H
ATOM 315 H2’2 PC B 10 -8.267 10.079 -8.298 1.00 0.60 H
ATOM 316 H1’1 PC B 10 -9.055 12.064 -7.189 1.00 0.70 H
ATOM 317 H5 PC B 10 -5.898 8.142 -4.095 1.00 0.60 H
ATOM 318 H6 PC B 10 -6.658 9.116 -6.192 1.00 0.66 H
ATOM 319 HN41 PC B 10 -2.403 8.438 -2.968 1.00 0.52 H
ATOM 320 HN42 PC B 10 -4.030 7.949 -2.553 1.00 0.60 H
ATOM 321 C8’ PT B 11 -1.203 7.673 -9.300 1.00 0.37 C
ATOM 322 C7’ PT B 11 -1.154 6.721 -10.504 1.00 0.42 C
ATOM 323 O7’ PT B 11 -0.775 5.587 -10.324 1.00 0.51 O
ATOM 324 C5’ PT B 11 -1.368 6.143 -12.883 1.00 0.47 C
ATOM 325 C’ PT B 11 -0.037 5.388 -13.063 1.00 0.45 C
ATOM 326 O1’ PT B 11 0.769 5.748 -13.900 1.00 0.48 O
ATOM 327 N4’ PT B 11 -1.497 7.108 -11.727 1.00 0.42 N
ATOM 328 C3’ PT B 11 -2.015 8.494 -11.985 1.00 0.44 C
ATOM 329 C2’ PT B 11 -3.334 8.420 -12.776 1.00 0.52 C
ATOM 330 N1’ PT B 11 -4.484 8.907 -11.937 1.00 0.49 N
ATOM 331 N1 PT B 11 -1.516 7.069 -7.995 1.00 0.34 N
ATOM 332 C6 PT B 11 -2.806 6.796 -7.669 1.00 0.37 C
ATOM 333 C2 PT B 11 -0.467 6.723 -7.160 1.00 0.32 C
ATOM 334 O2 PT B 11 0.706 6.949 -7.443 1.00 0.33 O
ATOM 335 N3 PT B 11 -0.817 6.082 -5.991 1.00 0.32 N
ATOM 336 C4 PT B 11 -2.097 5.763 -5.586 1.00 0.35 C
ATOM 337 O4 PT B 11 -2.288 5.199 -4.511 1.00 0.40 O
ATOM 338 C5 PT B 11 -3.126 6.163 -6.522 1.00 0.38 C
ATOM 339 C5M PT B 11 -4.584 5.811 -6.238 1.00 0.46 C
ATOM 340 H8’1 PT B 11 -1.952 8.442 -9.488 1.00 0.41 H
ATOM 341 H8’2 PT B 11 -0.230 8.157 -9.222 1.00 0.38 H
ATOM 342 H5’1 PT B 11 -1.547 6.704 -13.799 1.00 0.53 H
ATOM 343 H5’2 PT B 11 -2.159 5.399 -12.786 1.00 0.49 H
ATOM 344 H3’1 PT B 11 -2.189 9.007 -11.039 1.00 0.41 H
ATOM 345 H3’2 PT B 11 -1.279 9.052 -12.564 1.00 0.50 H
ATOM 346 H2’1 PT B 11 -3.519 7.387 -13.072 1.00 0.57 H
ATOM 347 H2’2 PT B 11 -3.254 9.038 -13.670 1.00 0.63 H
ATOM 348 H1’1 PT B 11 -4.339 9.698 -11.202 1.00 0.47 H
ATOM 349 H6 PT B 11 -3.595 7.092 -8.362 1.00 0.44 H
ATOM 350 HN3 PT B 11 -0.063 5.800 -5.382 1.00 0.37 H
ATOM 351 HM51 PT B 11 -5.235 6.416 -6.868 1.00 1.09 H
ATOM 352 HM52 PT B 11 -4.808 6.007 -5.189 1.00 1.18 H
ATOM 353 HM53 PT B 11 -4.749 4.756 -6.453 1.00 1.04 H
…

RTP:

[ PC ]
[ atoms ]
N1’ N -0.40300 1
H1’1 H 0.28420 2
C2’ CT -0.12410 3
H2’1 H1 0.11470 4
H2’2 H1 0.11470 5
C3’ CT -0.05220 6
H3’1 H1 0.10330 7
H3’2 H1 0.10330 8
N4’ N -0.09410 9
C5’ CT -0.11120 10
H5’1 H1 0.06780 11
H5’2 H1 0.06780 12
C’ C 0.62090 13
O1’ O -0.58070 14
C7’ C 0.43910 15
O7’ O -0.55020 16
C8’ CT -0.17690 17
H8’1 H1 0.11160 18
H8’2 H1 0.11160 19
N1 N* -0.05860 20
C2 C 0.85040 21
O2 O -0.61640 22
N3 NC -0.80620 23
C4 CA 0.89360 24
N4 N2 -0.99410 25
HN41 H 0.42670 26
HN42 H 0.42670 27
C5 CM -0.53600 28
H5 HA 0.20510 29
C6 CM -0.05670 30
H6 H4 0.21890 31
[ bonds ]
N1’ H1’1
N1’ C2’
C2’ H2’1
C2’ H2’2
C2’ C3’
C3’ H3’1
C3’ H3’2
C3’ N4’
N4’ C5’
N4’ C7’
C5’ H5’1
C5’ H5’2
C5’ C’
C’ O1’
C7’ O7’
C7’ C8’
C8’ H8’1
C8’ H8’2
C8’ N1
N1 C2
N1 C6
C2 O2
C2 N3
N3 C4
C4 N4
C4 C5
N4 HN41
N4 HN42
C5 H5
C5 C6
C6 H6
[ impropers ]
C2 C6 N1 C8’
N1 N3 C2 O2
C4 HN41 N4 HN42
N1 C5 C6 H6
C6 C4 C5 H5
C5 N4 C4 N3

Does anyone know why this is happening?

I searched in the forum for an answer to this mystery, but I can’t seem to find any clues (or maybe I’m bad at searching…)

I would be very happy to learn what I’m doing wrong here.

Thank you for reading!

Best regards
Jimmy

2

Does the previous residue in the chain refer to +N9 or does the succeeding residue refer to -N9 in any of their bonded interactions?

3

Hello, thank you for the reply!

So yes, there is an atom N9 in the previous residue PG9. If I understood your question correctly, you were asking if there is an atom +N9 or -N9 in the residue. But I couldn’t find any atom names in the PDB file (it’s written in the previous post) nor in the rtp file. This is the rtp file for PG & NPG:

[ PG ] ; edited from DG
[ atoms ]
N1’ N -0.40300 1
H1’1 H 0.28420 2
C2’ CT -0.12410 3
H2’1 H1 0.11470 4
H2’2 H1 0.11470 5
C3’ CT -0.05220 6
H3’1 H1 0.10330 7
H3’2 H1 0.10330 8
N4’ N -0.09410 9
C5’ CT -0.11120 10
H5’1 H1 0.06780 11
H5’2 H1 0.06780 12
C’ C 0.62090 13
O1’ O -0.58070 14
C7’ C 0.43910 15
O7’ O -0.55020 16
C8’ CT -0.23590 17
H8’1 H1 0.14180 18
H8’2 H1 0.14180 19
N9 N* 0.02680 20
C8 CK 0.08620 21
H8 H5 0.16230 22
N7 NB -0.53770 23
C6 C 0.40750 24
O6 O -0.52950 25
C5 CB 0.23190 26
C4 CB 0.08820 27
N3 NC -0.36510 28
C2 CA 0.46200 29
N2 N2 -0.87750 30
HN21 H 0.40420 31
HN22 H 0.40420 32
N1 NA -0.32510 33
HN1 H 0.31360 34
[ bonds ]
N1’ H1’1
N1’ C2’
C2’ H2’1
C2’ H2’2
C2’ C3’
C3’ H3’1
C3’ H3’2
C3’ N4’
N4’ C5’
N4’ C7’
C5’ H5’1
C5’ H5’2
C5’ C’
C’ O1’
C7’ O7’
C7’ C8’
C8’ H8’1
C8’ H8’2
C8’ N9
N9 C8
N9 C4
C8 H8
C8 N7
N7 C5
C6 O6
C6 C5
C6 N1
C5 C4
C4 N3
N3 C2
C2 N2
C2 N1
N2 HN21
N2 HN22
N1 HN1
[ impropers ]
C4 C8 N9 C8’
C5 N1 C6 O6
C6 C2 N1 HN1
C2 HN21 N2 HN22
N9 N7 C8 H8
N2 N1 C2 N3

[ NPG ] ; edited from DG5
[ atoms ]
N1’ N3 0.00490 1
H1’1 H 0.25310 2
H1’2 H 0.25310 3
H1’3 H 0.25310 4
C2’ CT 0.07230 5
H2’1 HP 0.08190 6
H2’2 HP 0.08190 7
C3’ CT -0.06060 8
H3’1 H1 0.08940 9
H3’2 H1 0.08940 10
N4’ N -0.06150 11
C5’ CT -0.12510 12
H5’1 H1 0.06740 13
H5’2 H1 0.06740 14
C’ C 0.61400 15
O1’ O -0.57540 16
C7’ C 0.45000 17
O7’ O -0.55980 18
C8’ CT -0.20610 19
H8’1 H1 0.13470 20
H8’2 H1 0.13470 21
N9 N* 0.01490 22
C8 CK 0.09080 23
H8 H5 0.16180 24
N7 NB -0.54040 25
C6 C 0.40420 26
O6 O -0.52900 27
C5 CB 0.24100 28
C4 CB 0.07950 29
N3 NC -0.36220 30
C2 CA 0.45640 31
N2 N2 -0.87110 32
HN21 H 0.40240 33
HN22 H 0.40240 34
N1 NA -0.32290 35
HN1 H 0.31340 36
[ bonds ]
N1’ H1’1
N1’ H1’2
N1’ H1’3
N1’ C2’
C2’ H2’1
C2’ H2’2
C2’ C3’
C3’ H3’1
C3’ H3’2
C3’ N4’
N4’ C5’
N4’ C7’
C5’ H5’1
C5’ H5’2
C5’ C’
C’ O1’
C7’ O7’
C7’ C8’
C8’ H8’1
C8’ H8’2
C8’ N9
N9 C8
N9 C4
C8 H8
C8 N7
N7 C5
C6 O6
C6 C5
C6 N1
C5 C4
C4 N3
N3 C2
C2 N2
C2 N1
N2 HN21
N2 HN22
N1 HN1
[ impropers ]
C4 C8 N9 C8’
C5 N1 C6 O6
C6 C2 N1 HN1
C2 HN21 N2 HN22
N9 N7 C8 H8
N2 N1 C2 N3

As you can see, the atom type for N9 is defined as N*.
Also, I’m not sure if this is relevant, but I added a new angle definition concerned with N* in ffbonded.itp:

[ angletypes ]
…
C CT N* 1 110.130 209.200 ; FF cst by analogy to CT-CT-N*; Eq.val. from QM geo.opt.

And these is the first two residues of the PNA structure I’m trying to read.

image
image600×600 58.6 KB

Lastly, this is the actual command I used for pdb2gmx:

gmx_mpi pdb2gmx -f PNA.pdb -o test.gro -v -ignh

Thank you for reading!

Best regards,
Jimmy

4

Could there be a problem with assigning the atom name N9 in the previous/succeeding residues?