Unable to generate topol.top, porse.itp and protein.gro file

User discussions
1

GROMACS version:2021.1
GROMACS modification: No
I am using CHARMM36-july2021 forcefield. but it is show the error when I am giving : gmx pdb2gmx -f 1AKI_clean.pdb -o 1AKI_processed.gro command.
it is showing this error

Command line:
gmx pdb2gmx -f apomb.pdb -o 1yamb_processed.gro

Select the Force Field:

From current directory:

1: CHARMM36 all-atom force field

2: CHARMM36 all-atom force field

From ‘/usr/local/gromacs/share/gromacs/top’:

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

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

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

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

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

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

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

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

11: GROMOS96 43a1 force field

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

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

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

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

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

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

Using the Charmm36-jul2021 (1) force field in directory ./charmm36-jul2021 (1).ff
Opening force field file ./charmm36-jul2021 (1).ff/watermodels.dat

Select the Water Model:

1: TIP3P_CHARMM CHARMM-modified TIP3P water model (recommended over original TIP3P)

2: TIP3P 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
6

going to rename ./charmm36-jul2021 (1).ff/aminoacids.r2b
Opening force field file ./charmm36-jul2021 (1).ff/aminoacids.r2b

going to rename ./charmm36-jul2021 (1).ff/carb.r2b
Opening force field file ./charmm36-jul2021 (1).ff/carb.r2b

going to rename ./charmm36-jul2021 (1).ff/cgenff.r2b
Opening force field file ./charmm36-jul2021 (1).ff/cgenff.r2b

going to rename ./charmm36-jul2021 (1).ff/ethers.r2b
Opening force field file ./charmm36-jul2021 (1).ff/ethers.r2b

going to rename ./charmm36-jul2021 (1).ff/lipid.r2b
Opening force field file ./charmm36-jul2021 (1).ff/lipid.r2b

going to rename ./charmm36-jul2021 (1).ff/metals.r2b
Opening force field file ./charmm36-jul2021 (1).ff/metals.r2b

going to rename ./charmm36-jul2021 (1).ff/na.r2b
Opening force field file ./charmm36-jul2021 (1).ff/na.r2b

going to rename ./charmm36-jul2021 (1).ff/silicates.r2b
Opening force field file ./charmm36-jul2021 (1).ff/silicates.r2b

going to rename ./charmm36-jul2021 (1).ff/solvent.r2b
Opening force field file ./charmm36-jul2021 (1).ff/solvent.r2b
Reading apomb.pdb…
Read ‘’, 1199 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 153 residues with 1199 atoms

chain #res #atoms

1 ‘A’ 153 1199

All occupancies are one
All occupancies are one
Opening force field file ./charmm36-jul2021 (1).ff/atomtypes.atp

Reading residue database… (Charmm36-jul2021 (1))
Opening force field file ./charmm36-jul2021 (1).ff/aminoacids.rtp
Opening force field file ./charmm36-jul2021 (1).ff/carb.rtp
Opening force field file ./charmm36-jul2021 (1).ff/cgenff.rtp
Opening force field file ./charmm36-jul2021 (1).ff/ethers.rtp
Opening force field file ./charmm36-jul2021 (1).ff/lipid.rtp
Opening force field file ./charmm36-jul2021 (1).ff/metals.rtp
Opening force field file ./charmm36-jul2021 (1).ff/na.rtp
Opening force field file ./charmm36-jul2021 (1).ff/silicates.rtp
Opening force field file ./charmm36-jul2021 (1).ff/solvent.rtp
Opening force field file ./charmm36-jul2021 (1).ff/aminoacids.hdb
Opening force field file ./charmm36-jul2021 (1).ff/carb.hdb
Opening force field file ./charmm36-jul2021 (1).ff/cgenff.hdb
Opening force field file ./charmm36-jul2021 (1).ff/ethers.hdb
Opening force field file ./charmm36-jul2021 (1).ff/lipid.hdb
Opening force field file ./charmm36-jul2021 (1).ff/metals.hdb
Opening force field file ./charmm36-jul2021 (1).ff/na.hdb
Opening force field file ./charmm36-jul2021 (1).ff/silicates.hdb
Opening force field file ./charmm36-jul2021 (1).ff/solvent.hdb
Opening force field file ./charmm36-jul2021 (1).ff/aminoacids.n.tdb
Opening force field file ./charmm36-jul2021 (1).ff/carb.n.tdb
Opening force field file ./charmm36-jul2021 (1).ff/cgenff.n.tdb
Opening force field file ./charmm36-jul2021 (1).ff/ethers.n.tdb
Opening force field file ./charmm36-jul2021 (1).ff/lipid.n.tdb
Opening force field file ./charmm36-jul2021 (1).ff/metals.n.tdb
Opening force field file ./charmm36-jul2021 (1).ff/na.n.tdb
Opening force field file ./charmm36-jul2021 (1).ff/silicates.n.tdb
Opening force field file ./charmm36-jul2021 (1).ff/solvent.n.tdb
Opening force field file ./charmm36-jul2021 (1).ff/aminoacids.c.tdb
Opening force field file ./charmm36-jul2021 (1).ff/carb.c.tdb
Opening force field file ./charmm36-jul2021 (1).ff/cgenff.c.tdb
Opening force field file ./charmm36-jul2021 (1).ff/ethers.c.tdb
Opening force field file ./charmm36-jul2021 (1).ff/lipid.c.tdb
Opening force field file ./charmm36-jul2021 (1).ff/metals.c.tdb
Opening force field file ./charmm36-jul2021 (1).ff/na.c.tdb
Opening force field file ./charmm36-jul2021 (1).ff/silicates.c.tdb
Opening force field file ./charmm36-jul2021 (1).ff/solvent.c.tdb

Back Off! I just backed up topol.top to ./#topol.top.2#

Processing chain 1 ‘A’ (1199 atoms, 153 residues)
Analysing hydrogen-bonding network for automated assignment of histidine
protonation. 224 donors and 217 acceptors were found.
There are 279 hydrogen bonds
Will use HISD for residue 24
Will use HISE for residue 36
Will use HISE for residue 48
Will use HISE for residue 64
Will use HISE for residue 81
Will use HISE for residue 82
Will use HISE for residue 93
Will use HISE for residue 97
Will use HISE for residue 113
Will use HISE for residue 116
Will use HISE for residue 119

Identified residue GLY1 as a starting terminus.

Identified residue GLY153 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Special Atom Distance matrix:
HIS24 HIS36 HIS48 MET55 HIS64 HIS81 HIS82
NE2184 NE2280 NE2387 SD441 NE2515 NE2633 NE2643
HIS36 NE2280 1.862
HIS48 NE2387 2.364 2.067
MET55 SD441 1.778 1.291 0.893
HIS64 NE2515 1.729 1.624 1.371 1.277
HIS81 NE2633 2.709 3.105 4.100 3.710 2.746
HIS82 NE2643 2.260 2.287 3.298 2.908 1.952 0.919
HIS93 NE2728 2.037 1.598 1.898 1.721 0.645 2.370 1.504
HIS97 NE2759 2.411 1.965 1.816 1.872 0.769 2.686 1.859
HIS113 NE2893 1.224 1.084 2.297 1.426 2.010 3.295 2.662
HIS116 NE2918 1.211 1.540 3.014 2.194 2.353 2.735 2.292
HIS119 NE2943 0.297 1.990 2.643 2.019 2.003 2.710 2.334
MET131 SD1020 1.062 1.692 2.856 2.228 1.797 1.815 1.363
HIS93 HIS97 HIS113 HIS116 HIS119
NE2728 NE2759 NE2893 NE2918 NE2943
HIS97 NE2759 0.493
HIS113 NE2893 2.218 2.615
HIS116 NE2918 2.405 2.876 0.901
HIS119 NE2943 2.267 2.663 1.256 1.074
MET131 SD1020 1.740 2.211 1.516 1.034 1.050
Start terminus GLY-1: GLY-NH3+
End terminus GLY-153: COO-
Opening force field file ./charmm36-jul2021 (1).ff/aminoacids.arn

Checking for duplicate atoms…

Generating any missing hydrogen atoms and/or adding termini.

Program: gmx pdb2gmx, version 2021.1
Source file: src/gromacs/gmxpreprocess/pgutil.cpp (line 151)

Fatal error:
Residue 153 named GLY of a molecule in the input file was mapped
to an entry in the topology database, but the atom CB used in
that entry is not found in the input file. Perhaps your atom
and/or residue naming needs to be fixed.

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

npp@npp-Precision-3650-Tower:~/subhasree_phd$

Please help me with this

2

Dear Subhasree,

This is a known bug of that release of the GROMACS port of the CHARMM36 force field, occurring if COO- terminus is selected and the last residue is a glycine. It has been reported here: Newest CHARMM36 port for GROMACS - #7 by jalemkul. Until the next release of the port, where this will be fixed, you can use the workaround suggested there.

Kind regards and sorry for the inconvenience,

Andras

3

dear Andras,
thank you so much for your continuous support and suggestion. i want to know exactly what i have in the pdb file. I am attaching the file. could you please help me with this.

thanks and regards,
Subhasree
1yamb.dat (186.2 KB)

4

Hi Subhasree,

you have the atoms in the pdb file. There are many different tools to analyze them. You can either print out the contents with the “cat” or “less” commands in the Linux command line, or use some graphical application (VMD, PyMOL etc.) to visualize the structure. GROMACS, being an MD engine, does not include such a tool, so this is somewhat out of the scope of this forum.

Hope that helps. Kind regards,

Andras