GROMACS version: 2022.5
GROMACS modification: No
Hi everyone (sorry this is going to be a long post)
I am trying to generate the topology for a ligand which is two glutathione moieties held together with a cadmium molecule using Charmms forcefield. The ligand molecule looks like this:
Starting from the beginning, I got the coordinates for this ligand from the PDB entry 8YR3. I am pasting the PDB coordinates of this ligand below:
HETATM 1 N1 GSH A 901 109.746 109.362 98.189 1.00179.52 N
HETATM 2 CA1 GSH A 901 109.662 110.356 99.231 1.00175.09 C
HETATM 3 C1 GSH A 901 108.375 111.086 99.090 1.00176.37 C
HETATM 4 O11 GSH A 901 107.844 111.145 97.966 1.00175.82 O
HETATM 5 O12 GSH A 901 107.883 111.606 100.103 1.00179.55 O
HETATM 6 CB1 GSH A 901 110.788 111.348 99.049 1.00171.03 C
HETATM 7 CG1 GSH A 901 110.797 112.380 100.161 1.00167.89 C
HETATM 8 CD1 GSH A 901 111.609 111.824 101.289 1.00169.81 C
HETATM 9 OE1 GSH A 901 111.707 110.622 101.413 1.00171.78 O
HETATM 10 N2 GSH A 901 112.194 112.702 102.097 1.00172.59 N
HETATM 11 CA2 GSH A 901 112.834 112.276 103.318 1.00175.39 C
HETATM 12 C2 GSH A 901 111.921 111.306 103.987 1.00171.66 C
HETATM 13 O2 GSH A 901 110.722 111.373 103.800 1.00172.51 O
HETATM 14 CB2 GSH A 901 113.120 113.455 104.247 1.00181.59 C
HETATM 15 SG2 GSH A 901 114.733 114.267 104.045 1.00188.64 S
HETATM 16 N3 GSH A 901 112.481 110.400 104.770 1.00173.87 N
HETATM 17 CA3 GSH A 901 111.862 110.041 106.025 1.00179.04 C
HETATM 18 C3 GSH A 901 110.491 109.486 105.770 1.00184.61 C
HETATM 19 O31 GSH A 901 110.401 108.357 105.256 1.00187.35 O
HETATM 20 O32 GSH A 901 109.506 110.191 106.056 1.00186.74 O
HETATM 21 CD CD2 A 902 116.210 116.207 104.438 1.00324.75 Cd
HETATM 22 N1 GSH B 901 123.626 122.999 98.818 1.00179.52 N
HETATM 23 CA1 GSH B 901 123.752 121.676 99.373 1.00175.09 C
HETATM 24 C1 GSH B 901 124.667 120.884 98.496 1.00176.37 C
HETATM 25 O11 GSH B 901 124.829 121.291 97.332 1.00175.82 O
HETATM 26 O12 GSH B 901 125.243 119.884 98.962 1.00179.55 O
HETATM 27 CB1 GSH B 901 122.363 121.080 99.399 1.00171.03 C
HETATM 28 CG1 GSH B 901 122.197 120.146 100.581 1.00167.89 C
HETATM 29 CD1 GSH B 901 120.879 120.502 101.196 1.00169.81 C
HETATM 30 OE1 GSH B 901 120.396 121.587 100.952 1.00171.78 O
HETATM 31 N2 GSH B 901 120.299 119.623 102.005 1.00172.59 N
HETATM 32 CA2 GSH B 901 119.620 120.109 103.180 1.00175.39 C
HETATM 33 C2 GSH B 901 120.481 121.176 103.765 1.00171.66 C
HETATM 34 O2 GSH B 901 121.691 121.107 103.669 1.00172.51 O
HETATM 35 CB2 GSH B 901 119.376 119.000 104.201 1.00181.59 C
HETATM 36 SG2 GSH B 901 117.801 118.107 104.049 1.00188.64 S
HETATM 37 N3 GSH B 901 119.867 122.171 104.381 1.00173.87 N
HETATM 38 CA3 GSH B 901 120.239 122.535 105.728 1.00179.04 C
HETATM 39 C3 GSH B 901 121.703 122.864 105.787 1.00184.61 C
HETATM 40 O31 GSH B 901 122.102 123.886 105.201 1.00187.35 O
HETATM 41 O32 GSH B 901 122.461 122.091 106.401 1.00186.74 O
CONECT 1 2
CONECT 2 1 3 6
CONECT 3 2 4 5
CONECT 4 3
CONECT 5 3
CONECT 6 2 7
CONECT 7 6 8
CONECT 8 7 9 10
CONECT 9 8
CONECT 10 8 11
CONECT 11 10 12 14
CONECT 12 11 13 16
CONECT 13 12
CONECT 14 11 15
CONECT 15 14 21
CONECT 16 12 17
CONECT 17 16 18
CONECT 18 17 19 20
CONECT 19 18
CONECT 20 18
CONECT 21 15 36
CONECT 22 23
CONECT 23 22 24 27
CONECT 24 23 25 26
CONECT 25 24
CONECT 26 24
CONECT 27 23 28
CONECT 28 27 29
CONECT 29 28 30 31
CONECT 30 29
CONECT 31 29 32
CONECT 32 31 33 35
CONECT 33 32 34 37
CONECT 34 33
CONECT 35 32 36
CONECT 36 35 21
CONECT 37 33 38
CONECT 38 37 39
CONECT 39 38 40 41
CONECT 40 39
CONECT 41 39
END
Since, glutathione is made up of 3 amino acids glutamate, cysteine and glycine, I tried to rename the atoms for these amino acids according to the top_all36_prot file in the charmm directory. Since Charmms forcefield has cadmium but only as an ion, I was thinking I can treat cadmium as a non-covalently bound ion. Thats why I used negatively charged cysteines (CYM) here. I also added the TER delimiters to my pdb. The modified file looks like this:
ATOM 1 N GLU A 901 109.746 109.362 98.189 1.00179.52 N
ATOM 2 CA GLU A 901 109.662 110.356 99.231 1.00175.09 C
ATOM 3 C GLU A 901 108.375 111.086 99.090 1.00176.37 C
ATOM 4 OT1 GLU A 901 107.844 111.145 97.966 1.00175.82 O
ATOM 5 OT2 GLU A 901 107.883 111.606 100.103 1.00179.55 O
ATOM 6 CB GLU A 901 110.788 111.348 99.049 1.00171.03 C
ATOM 7 CG GLU A 901 110.797 112.380 100.161 1.00167.89 C
ATOM 8 CD GLU A 901 111.609 111.824 101.289 1.00169.81 C
ATOM 9 OE1 GLU A 901 111.707 110.622 101.413 1.00171.78 O
ATOM 10 N CYM A 901 112.194 112.702 102.097 1.00172.59 N
ATOM 11 CA CYM A 901 112.834 112.276 103.318 1.00175.39 C
ATOM 12 C CYM A 901 111.921 111.306 103.987 1.00171.66 C
ATOM 13 O CYM A 901 110.722 111.373 103.800 1.00172.51 O
ATOM 14 CB CYM A 901 113.120 113.455 104.247 1.00181.59 C
ATOM 15 SG CYM A 901 114.733 114.267 104.045 1.00188.64 S
ATOM 16 N GLY A 901 112.481 110.400 104.770 1.00173.87 N
ATOM 17 CA GLY A 901 111.862 110.041 106.025 1.00179.04 C
ATOM 18 C GLY A 901 110.491 109.486 105.770 1.00184.61 C
ATOM 19 O GLY A 901 110.401 108.357 105.256 1.00187.35 O
ATOM 20 O GLY A 901 109.506 110.191 106.056 1.00186.74 O
TER
HETATM 21 CD CD2 A 902 116.210 116.207 104.438 1.00324.75 Cd
TER
ATOM 22 N GLU B 901 123.626 122.999 98.818 1.00179.52 N
ATOM 23 CA GLU B 901 123.752 121.676 99.373 1.00175.09 C
ATOM 24 C GLU B 901 124.667 120.884 98.496 1.00176.37 C
ATOM 25 OT1 GLU B 901 124.829 121.291 97.332 1.00175.82 O
ATOM 26 OT2 GLU B 901 125.243 119.884 98.962 1.00179.55 O
ATOM 27 CB GLU B 901 122.363 121.080 99.399 1.00171.03 C
ATOM 28 CG GLU B 901 122.197 120.146 100.581 1.00167.89 C
ATOM 29 CD GLU B 901 120.879 120.502 101.196 1.00169.81 C
ATOM 30 OE1 GLU B 901 120.396 121.587 100.952 1.00171.78 O
ATOM 31 N CYM B 901 120.299 119.623 102.005 1.00172.59 N
ATOM 32 CA CYM B 901 119.620 120.109 103.180 1.00175.39 C
ATOM 33 C CYM B 901 120.481 121.176 103.765 1.00171.66 C
ATOM 34 O CYM B 901 121.691 121.107 103.669 1.00172.51 O
ATOM 35 CB CYM B 901 119.376 119.000 104.201 1.00181.59 C
ATOM 36 SG CYM B 901 117.801 118.107 104.049 1.00188.64 S
ATOM 37 N GLY B 901 119.867 122.171 104.381 1.00173.87 N
ATOM 38 CA GLY B 901 120.239 122.535 105.728 1.00179.04 C
ATOM 39 C GLY B 901 121.703 122.864 105.787 1.00184.61 C
ATOM 40 O GLY B 901 122.102 123.886 105.201 1.00187.35 O
ATOM 41 O GLY B 901 122.461 122.091 106.401 1.00186.74 O
TER
CONECT 1 2
CONECT 2 1 3 6
CONECT 3 2 4 5
CONECT 4 3
CONECT 5 3
CONECT 6 2 7
CONECT 7 6 8
CONECT 8 7 9 10
CONECT 9 8
CONECT 10 8 11
CONECT 11 10 12 14
CONECT 12 11 13 16
CONECT 13 12
CONECT 14 11 15
CONECT 15 14 21
CONECT 16 12 17
CONECT 17 16 18
CONECT 18 17 19 20
CONECT 19 18
CONECT 20 18
CONECT 21 15 36
CONECT 22 23
CONECT 23 22 24 27
CONECT 24 23 25 26
CONECT 25 24
CONECT 26 24
CONECT 27 23 28
CONECT 28 27 29
CONECT 29 28 30 31
CONECT 30 29
CONECT 31 29 32
CONECT 32 31 33 35
CONECT 33 32 34 37
CONECT 34 33
CONECT 35 32 36
CONECT 36 35 21
CONECT 37 33 38
CONECT 38 37 39
CONECT 39 38 40 41
CONECT 40 39
CONECT 41 39
END
Now there are two problems that I am facing. First, when I tried to go ahead with this pdb file, pdb2gmx threw the following error:
Command line:
gmx pdb2gmx -f GSSGCDtestligand.pdb -o Ligand.pdb
Select the Force Field:
From current directory:
1: CHARMM all-atom force field
From ‘/opt/ohpc/pub/apps/gromacs/2022.5/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
1
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 GSSGCDtestligand.pdb…
WARNING: all CONECT records are ignored
Read ‘ATP-BINDING CASSETTE SUB-FAMILY B MEMBER 6; 5 TRANSPORTER 3,MT-ABC TRANSPORTER 3,P-GLYCOPROTEIN-RELATED PROTEIN,; 6 UBIQUITOUSLY-EXPRESSED MAMMALIAN ABC HALF TRANSPORTER’, 41 atoms
Analyzing pdb file
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 GSSGCDtestligand.pdb…
WARNING: all CONECT records are ignored
Read ‘ATP-BINDING CASSETTE SUB-FAMILY B MEMBER 6; 5 TRANSPORTER 3,MT-ABC TRANSPORTER 3,P-GLYCOPROTEIN-RELATED PROTEIN,; 6 UBIQUITOUSLY-EXPRESSED MAMMALIAN ABC HALF TRANSPORTER’, 41 atoms
Analyzing pdb file
Splitting chemical chains based on TER records or chain id changing.
Chain identifier ‘A’ is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file.
Chain identifier ‘A’ is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file.
There are 3 chains and 0 blocks of water and 7 residues with 41 atoms
chain #res #atoms
1 ‘A’ 3 20
2 ‘A’ 1 1
3 ‘B’ 3 20
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.1#
Processing chain 1 ‘A’ (20 atoms, 3 residues)
Identified residue GLU901 as a starting terminus.
Identified residue GLY901 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Start terminus GLU-901: NH3+
End terminus GLY-901: COO-
Opening force field file ./charmm36-jul2022.ff/aminoacids.arn
Program: gmx pdb2gmx, version 2022.5
Source file: src/gromacs/gmxpreprocess/pdb2gmx.cpp (line 873)
Fatal error:
Atom OT1 in residue GLU 901 was not found in rtp entry GLU with 17 atoms
while sorting atoms.
.
For more information and tips for troubleshooting, please check the GROMACS
website at Common Errors — GROMACS webpage https://www.gromacs.org documentation
I kind of understand what’s happening here. The Two oxygens linked to the Carbon right next to the NH3 of glutamate are not getting recognized. Can some one help me with this issue please.
My second question is there is a unusual bond involved here that is the specific peptide bond formed between the gamma-carboxyl group of glutamic acid and the amino group of cysteine. How can I define this bond? What are the files that I need to modify and with what information?
Pdb2gmx could not solve both these problems. I got an output but the ligand geometry was wrong as it could not make this bond and the ligand molecule appears to be broken between glutamate and cysteine. Also one of the O groups from the glutamate were also missing (question one). (See picture below).
I am a beginner and will be grateful if I can get the solutions to these questions.
Many thanks in advance