Gromacs error adding a number 1 to an atom

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Hello,

I have a PDB file that I am trying to run through Charmm36 FF. I had issues running it through the CHARMM-GUI, as it kept breaking bond and creating them that were not present. I am adding CARBS to the rtp and hdp files to run my special glycans and ligands through. However, I encountered this problem:

Program: gmx pdb2gmx, version 2022.4
Source file: src/gromacs/gmxpreprocess/add_par.cpp (line 165)

Fatal error:
Atom H611 not found in rtp database in residue BMA, it looks a bit like H61

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

I deleted all the hydrogens in the PDB file and these are my rtp and hdp additions for BMA that do not have H611
HDP:
BMA 10
1 5 H1 C1 C2 O5 C3
1 5 H5 C5 C4 C6 O5
1 5 H2 C2 C1 C3 O2
1 2 HO2 O2 C2 C1
1 5 H3 C3 C2 C4 O3
1 2 HO3 O3 C3 C2
1 5 H4 C4 C3 C5 O4
1 2 HO4 O4 C4 C3
2 6 H61 C6 C5 O6
1 2 HO6 O6 C6 C5
RTP
[ BMA ]
; 4C1 beta-D-mannose
[ atoms ]
C1 CC3162 0.3400 1
H1 HCA1 0.0900 1
C2 CC3161 0.1400 2
H2 HCA1 0.0900 2
O2 OC311 -0.6500 2
HO2 HCP1 0.4200 2
C3 CC3161 0.1400 3
H3 HCA1 0.0900 3
O3 OC311 -0.6500 3
HO3 HCP1 0.4200 3
C4 CC3161 0.1400 4
H4 HCA1 0.0900 4
O4 OC311 -0.6500 4
HO4 HCP1 0.4200 4
C5 CC3163 0.1100 5
H5 HCA1 0.0900 5
O5 OC3C61 -0.4000 5
C6 CC321 0.0500 6
H61 HCA2 0.0900 6
H62 HCA2 0.0900 6
O6 OC311 -0.6500 6
HO6 HCP1 0.4200 6

[ bonds ]
C1 H1
C1 O5
C1 C2
C2 H2
C2 O2
O2 HO2
C2 C3
C3 H3
C3 O3
O3 HO3
C3 C4
C4 H4
C4 O4
O4 HO4
C4 C5
C5 H5
C5 C6
C6 H61
C6 H62
C6 O6
O6 HO6
C5 O5
PDB
HETATM 29 C1 BMA A 3 167.984 108.551 20.553 1.00 0.00 C
HETATM 30 C2 BMA A 3 168.272 109.712 21.507 1.00 0.00 C
HETATM 31 C3 BMA A 3 167.985 111.045 20.822 1.00 0.00 C
HETATM 32 C4 BMA A 3 168.623 111.116 19.458 1.00 0.00 C
HETATM 33 C5 BMA A 3 168.312 109.887 18.625 1.00 0.00 C
HETATM 34 C6 BMA A 3 169.047 109.926 17.345 1.00 0.00 C
HETATM 35 O2 BMA A 3 169.688 109.694 21.806 1.00 0.00 O
HETATM 36 O3 BMA A 3 168.482 112.149 21.597 1.00 0.00 O
HETATM 37 O4 BMA A 3 168.109 112.236 18.772 1.00 0.00 O
HETATM 38 O5 BMA A 3 168.699 108.700 19.377 1.00 0.00 O
HETATM 39 O6 BMA A 3 168.607 108.818 16.576 1.00 0.00 O

HETATM 198 C1 BMA D 3 171.978 116.240 30.177 1.00 0.00 C
HETATM 199 C2 BMA D 3 172.134 115.131 29.070 1.00 0.00 C
HETATM 200 C3 BMA D 3 173.629 114.843 28.775 1.00 0.00 C
HETATM 201 C4 BMA D 3 174.354 116.131 28.500 1.00 0.00 C
HETATM 202 C5 BMA D 3 174.159 117.098 29.673 1.00 0.00 C
HETATM 203 C6 BMA D 3 174.757 118.423 29.334 1.00 0.00 C
HETATM 204 O2 BMA D 3 171.541 115.561 27.862 1.00 0.00 O
HETATM 205 O3 BMA D 3 173.854 113.916 27.687 1.00 0.00 O
HETATM 206 O4 BMA D 3 175.762 115.873 28.307 1.00 0.00 O
HETATM 207 O5 BMA D 3 172.760 117.364 29.890 1.00 0.00 O
HETATM 208 O6 BMA D 3 174.386 119.288 30.386 1.00 0.00 O

Also, when I try to add the H611 in rtp, it just adds another 1, so H6111. I am unsure how to trouble shoot this. any help would be appreciated.

Heather

2

Hi,

Could you provide all the command-line options as well as the input options to pdb2gmx? Did you select any terminal modifications?

3

(mydirectory)/gromacs_peg# gmx pdb2gmx -f fixed_TEST4.3.pdb -o conf.gro
:-) GROMACS - gmx pdb2gmx, 2022.4 (-:

Executable: /usr/local/gromacs/bin/gmx
Data prefix: /usr/local/gromacs
Working dir: /(mydirectory)/desktop/gromacs_peg
Command line:
gmx pdb2gmx -f fixed_TEST4.3.pdb -o conf.gro

Select the Force Field:

From current directory:

1: CHARMM all-atom force field

From ‘/usr/local/gromacs/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-jul2022 force field in directory ./charmm36-jul2022.ff
Opening force field file ./charmm36-jul2022.ff/watermodels.dat

Select the Water Model:

1: TIP3P CHARMM-modified TIP3P water model (recommended over original TIP3P)

2: TIP3P_ORIGINAL Original TIP3P water model

3: SPC SPC water model

4: SPCE SPC/E water model

5: TIP5P TIP5P water model

6: TIP4P TIP4P water model

7: TIP4PEW TIP4P/Ew water model

8: None
8

going to rename ./charmm36-jul2022.ff/aminoacids.r2b
Opening force field file ./charmm36-jul2022.ff/aminoacids.r2b

going to rename ./charmm36-jul2022.ff/carb.r2b
Opening force field file ./charmm36-jul2022.ff/carb.r2b

going to rename ./charmm36-jul2022.ff/cgenff.r2b
Opening force field file ./charmm36-jul2022.ff/cgenff.r2b

going to rename ./charmm36-jul2022.ff/ethers.r2b
Opening force field file ./charmm36-jul2022.ff/ethers.r2b

going to rename ./charmm36-jul2022.ff/lipid.r2b
Opening force field file ./charmm36-jul2022.ff/lipid.r2b

going to rename ./charmm36-jul2022.ff/metals.r2b
Opening force field file ./charmm36-jul2022.ff/metals.r2b

going to rename ./charmm36-jul2022.ff/na.r2b
Opening force field file ./charmm36-jul2022.ff/na.r2b

going to rename ./charmm36-jul2022.ff/silicates.r2b
Opening force field file ./charmm36-jul2022.ff/silicates.r2b

going to rename ./charmm36-jul2022.ff/solvent.r2b
Opening force field file ./charmm36-jul2022.ff/solvent.r2b
Reading fixed_TEST4.3.pdb…
WARNING: all CONECT records are ignored
Read ‘’, 14475 atoms

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

There are 9 chains and 0 blocks of water and 1855 residues with 14475 atoms

chain #res #atoms

1 ‘A’ 8 98

2 ‘B’ 1 71

3 ‘D’ 6 74

4 ‘E’ 1 71

5 ‘G’ 448 3457

6 ‘H’ 448 3457

7 ‘I’ 214 1657

8 ‘J’ 214 1657

9 ‘K’ 515 3933

All occupancies are one
All occupancies are one
Opening force field file ./charmm36-jul2022.ff/atomtypes.atp

Reading residue database… (Charmm36-jul2022)
Opening force field file ./charmm36-jul2022.ff/aminoacids.rtp
Opening force field file ./charmm36-jul2022.ff/carb.rtp
Opening force field file ./charmm36-jul2022.ff/cgenff.rtp
Opening force field file ./charmm36-jul2022.ff/ethers.rtp
Opening force field file ./charmm36-jul2022.ff/lipid.rtp
Opening force field file ./charmm36-jul2022.ff/metals.rtp
Opening force field file ./charmm36-jul2022.ff/na.rtp
Opening force field file ./charmm36-jul2022.ff/silicates.rtp
Opening force field file ./charmm36-jul2022.ff/solvent.rtp
Opening force field file ./charmm36-jul2022.ff/aminoacids.hdb
Opening force field file ./charmm36-jul2022.ff/carb.hdb
Opening force field file ./charmm36-jul2022.ff/cgenff.hdb
Opening force field file ./charmm36-jul2022.ff/ethers.hdb
Opening force field file ./charmm36-jul2022.ff/lipid.hdb
Opening force field file ./charmm36-jul2022.ff/metals.hdb
Opening force field file ./charmm36-jul2022.ff/na.hdb
Opening force field file ./charmm36-jul2022.ff/silicates.hdb
Opening force field file ./charmm36-jul2022.ff/solvent.hdb
Opening force field file ./charmm36-jul2022.ff/aminoacids.n.tdb
Opening force field file ./charmm36-jul2022.ff/carb.n.tdb
Opening force field file ./charmm36-jul2022.ff/cgenff.n.tdb
Opening force field file ./charmm36-jul2022.ff/ethers.n.tdb
Opening force field file ./charmm36-jul2022.ff/lipid.n.tdb
Opening force field file ./charmm36-jul2022.ff/metals.n.tdb
Opening force field file ./charmm36-jul2022.ff/na.n.tdb
Opening force field file ./charmm36-jul2022.ff/silicates.n.tdb
Opening force field file ./charmm36-jul2022.ff/solvent.n.tdb
Opening force field file ./charmm36-jul2022.ff/aminoacids.c.tdb
Opening force field file ./charmm36-jul2022.ff/carb.c.tdb
Opening force field file ./charmm36-jul2022.ff/cgenff.c.tdb
Opening force field file ./charmm36-jul2022.ff/ethers.c.tdb
Opening force field file ./charmm36-jul2022.ff/lipid.c.tdb
Opening force field file ./charmm36-jul2022.ff/metals.c.tdb
Opening force field file ./charmm36-jul2022.ff/na.c.tdb
Opening force field file ./charmm36-jul2022.ff/silicates.c.tdb
Opening force field file ./charmm36-jul2022.ff/solvent.c.tdb

Back Off! I just backed up topol.top to ./#topol.top.12#

Processing chain 1 ‘A’ (98 atoms, 8 residues)

Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior.
8 out of 8 lines of specbond.dat converted successfully
Opening force field file ./charmm36-jul2022.ff/aminoacids.arn

Checking for duplicate atoms…

Generating any missing hydrogen atoms and/or adding termini.

Now there are 8 residues with 201 atoms
Chain time…

Back Off! I just backed up topol_Other_chain_A.itp to ./#topol_Other_chain_A.itp.6#

Making bonds…

Long Bond (1-3 = 0.347293 nm)

Long Bond (1-3 = 0.347293 nm)

Long Bond (30-32 = 0.398002 nm)

Long Bond (30-32 = 0.398002 nm)

Long Bond (103-105 = 0.298977 nm)

Long Bond (103-105 = 0.298977 nm)

Long Bond (154-156 = 0.432776 nm)

Long Bond (154-156 = 0.432776 nm)

atom O is missing in residue NAG 1 in the pdb file

atom O is missing in residue NAG 1 in the pdb file

atom O is missing in residue NAA 2 in the pdb file

atom O is missing in residue NAA 2 in the pdb file

Program: gmx pdb2gmx, version 2022.4
Source file: src/gromacs/gmxpreprocess/add_par.cpp (line 165)

Fatal error:
Atom H611 not found in rtp database in residue BMA, it looks a bit like H61

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

This is the full input as I am trying to convert the PDB to gro through the Charmm36 FF and run an implicit solvation simulation. The o in NAG and NAA are also concerning because I manually edited the O to O1 to satisfy. And added my own in hte hdb and rtp for the glycans due to PDB and CHARMM names having letter restrictions NAG= AGLCNA, NAA= BGLCNA, BMA= BMAN, MAN=AMAN, FUC=AFUC, NAB=a modified BGLCNA because it binds to the PEG. Also, it says long bonds? Is this the reason for the additional 1 on the H61 error? Should I manually correct this? Is this error from the conversion of PDB to CHARMM? Thank you for your help.

Heather

4

Also, for the residuetype.dat file. There is not one in the CHARMM36 ff file as I added that manually and tried to implicate that the glycans (i.e NAG, NAA, NAB, etc) are all other.

5

I must admit I’m not sure what’s going wrong. It would help with a reproducible example so that I could test it myself.

6

This is the expected behaviour, if more than one hydrogen are added to a heavy atom pdb2gmx will automatically index them (See: Doc. ).

This entry instructs pdb2gmx to create the atoms H611 and H612.

You can either edit your rtp or, If you want the atoms to be called H61 and H62 instead you need ot modify the entry to:

2 6 H6 C6 C5 O6

Hope that helps,
Best,
Florian

1 Like
8

This did help! Thank you so much

9

Hello,

I have a couple questions for you that is along the same lines as original question. I am adding the PEG now and it is large (1K). This is a section from the RTP file I generated from CGenFF:
1 3 H150 C61 C60 O62
1 3 H151 C63 C61 O62
1 3 H152 C63 C64 O65
1 3 H153 C64 C63 O65
1 3 H154 C64 C63 O65
1 3 H155 C66 C64 O65
1 3 H156 C66 C67 O68
1 3 H157 C67 C66 O68
1 3 H158 C67 C66 O68
1 3 H159 C69 C67 O68

Will the 150, cause issues with the expected behavior from Gromacs HDB to add 1, 2,3, etc.? So should I renumber the rtp to start at 151 instead of 150? And just subtract the third integer so the system can do its expected behavior?

Example:
1 3 H15 C61 C60 O62

My other question is from the documentation you linked in the comment. It mentions HDB is optional. Then I do not actually have to do HDB for the hydrogens if my RTP has them generated? Or because I am adding PEG to my RTP file, it be recommended to still include the HDB in this instance.

Thanks in advance,
Heather

10

Yes unfortunately you have to change your .rtp file. However there might be an easier way to include large organics polymers in GROMACS, especially when they consist of repeating subunits. This is not my subject area, so I don’t know, but it is worth investigating.

In regards to the second question: The .hdb is only necessary if you want to add hydrogens with pdb2gmx. If your starting structure already contains all necessary hydrogens you don’t need to make an .hdb entry. However, the hydrogens in the .rtp alone are not sufficient, in addition you need them either in your starting structure or in your .hdb file.

Best,
Florian