GROMACS version: 2022.3
GROMACS modification: No
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Hi,
I’m trying to create structure and topology files from my pdb using pdb2gmx, but receiving the error: ‘Residue ‘MPD’ not found in residue topology database’. MPD is a simple small molecule composed of carbon, hydrogen and oxygen and it is bound to my protein.
The structure was prepared using Schrodinger’s Protein Preparation Wizard. I would like to simulate the structure using the force field Amber14sb.
Here is the full error message:
Command line:
gmx pdb2gmx -f GMX_1y6w_fully_prepped.pdb -o 1y6w.gro -p 1y6w.top -water tip3p
Select the Force Field:
From current directory:
1: AMBER14SB
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)
pdb2gmx and x2top can’rt
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 Amber14sb force field in directory ./amber14sb.ff
going to rename ./amber14sb.ff/aminoacids.r2b
Opening force field file ./amber14sb.ff/aminoacids.r2b
going to rename ./amber14sb.ff/dna.r2b
Opening force field file ./amber14sb.ff/dna.r2b
going to rename ./amber14sb.ff/rna.r2b
Opening force field file ./amber14sb.ff/rna.r2b
Reading GMX_1y6w_fully_prepped.pdb…
WARNING: all CONECT records are ignored
Read ‘TRAPPED INTERMEDIATE OF CALMODULIN’, 2334 atoms
Analyzing pdb file
Splitting chemical chains based on TER records or chain id changing.
There are 4 chains and 1 blocks of water and 169 residues with 2334 atoms
chain #res #atoms
1 ‘A’ 150 2254
2 ‘A’ 4 4
3 ‘A’ 1 22
4 ‘A’ 1 15
5 ’ ’ 13 39 (only water)
there were 11 atoms with zero occupancy and 9 atoms with occupancy unequal to one (out of 2334 atoms). Check your pdb file.ZZ
there were 11 atoms with zero occupancy and 9 atoms with occupancy unequal to one (out of 2334 atoms). Check your pdb file.
Opening force field file ./amber14sb.ff/atomtypes.atp
Reading residue database… (Amber14sb)
Opening force field file ./amber14sb.ff/aminoacids.rtp
Opening force field file ./amber14sb.ff/dna.rtp
Opening force field file ./amber14sb.ff/rna.rtp
Opening force field file ./amber14sb.ff/aminoacids.hdb
Opening force field file ./amber14sb.ff/dna.hdb
Opening force field file ./amber14sb.ff/rna.hdb
Opening force field file ./amber14sb.ff/aminoacids.n.tdb
Opening force field file ./amber14sb.ff/aminoacids.c.tdb
Processing chain 1 ‘A’ (2254 atoms, 150 residues)
Identified residue ACE0 as a starting terminus.
Identified residue NME148 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Special Atom Distance matrix:
MET36 CYS41 MET51 MET71 MET72 CYS75 MET76
SD537 SG616 SD758 SD1049 SD1066 SG1116 SD1127
CYS41 SG616 0.667
MET51 SD758 0.478 0.722
MET71 SD1049 0.558 1.083 0.477
MET72 SD1066 0.507 0.545 0.756 0.862
CYS75 SG1116 0.535 0.204 0.528 0.916 0.558
MET76 SD1127 1.080 0.673 1.106 1.333 0.642 0.795
MET109 SD1644 3.645 3.096 3.330 3.767 3.549 3.137 3.118
MET124 SD1870 3.604 3.115 3.253 3.684 3.580 3.123 3.222
MET144 SD2176 3.047 2.631 2.682 3.110 3.104 2.605 2.853
MET145 SD2192 2.566 2.053 2.245 2.692 2.519 2.070 2.175
MET109 MET124 MET144
SD1644 SD1870 SD2176
MET124 SD1870 0.531
MET144 SD2176 1.138 0.740
MET145 SD2192 1.099 1.066 0.787
Linking CYS-41 SG-616 and CYS-75 SG-1116…
Opening force field file ./amber14sb.ff/aminoacids.arn
Opening force field file ./amber14sb.ff/dna.arn
Opening force field file ./amber14sb.ff/rna.arn
Checking for duplicate atoms…
Generating any missing hydrogen atoms and/or adding termini.
Now there are 150 residues with 2254 atoms
Chain time…
Making bonds…
Number of bonds was 2267, now 2267
Generating angles, dihedrals and pairs…
Before cleaning: 5903 pairs
Before cleaning: 5918 dihedrals
Making cmap torsions…
There are 5918 dihedrals, 447 impropers, 4083 angles
5873 pairs, 2267 bonds and 0 virtual sites
Total mass 16684.380 a.m.u.
Total charge -24.000 e
Writing topology
Processing chain 2 ‘A’ (4 atoms, 4 residues)
Residue CA149 has type ‘Ion’, assuming it is not linked into a chain.
Residue CA150 has type ‘Ion’, assuming it is not linked into a chain.
Residue CA151 has type ‘Ion’, assuming it is not linked into a chain.
Residue CA152 has type ‘Ion’, assuming it is not linked into a chain.
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 ./amber14sb.ff/aminoacids.arn
Opening force field file ./amber14sb.ff/dna.arn
Opening force field file ./amber14sb.ff/rna.arn
Checking for duplicate atoms…
Generating any missing hydrogen atoms and/or adding termini.
Now there are 4 residues with 4 atoms
Chain time…
Making bonds…
No bonds
Generating angles, dihedrals and pairs…
Making cmap torsions…
There are 0 dihedrals, 0 impropers, 0 angles
0 pairs, 0 bonds and 0 virtual sites
Total mass 160.320 a.m.u.
Total charge 8.000 e
Writing topology
Processing chain 3 ‘A’ (22 atoms, 1 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
Program: gmx pdb2gmx, version 2022.3
Source file: src/gromacs/gmxpreprocess/resall.cpp (line 617)
Fatal error:
Residue ‘MPD’ not found in residue topology database
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
/////////////////////////////////////////////////////////////////////
I isolated the MPD ligand and tried to use x2top to generate an rtp entry, but received this error:
Command line:
gmx x2top -f MPD.pdb -r MPD.rtp -ff select
Select the Force Field:
From current directory:
1: AMBER14SB
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
Opening force field /gromacs/top/oplsaa.ff/atomname2type.n2t
There are 23 name to type translations in file oplsaa.ff
Generating bonds from distances…
Can not find forcefield for atom C2-2 with 4 bonds
Program: gmx x2top, version 2022.3
Source file: src/gromacs/gmxpreprocess/x2top.cpp (line 180)
Fatal error:
Could only find a forcefield type for 21 out of 22 atoms
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
Any advice would be much appreciated.
Many thanks.