Molecular dynamic simulation of alkaloids

User discussions
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1

GROMACS version: 2023.3
GROMACS modification: Yes/No

So I am trying to make a simulation of an acid/base reaction involving an alkaloid. I generated .pdb, .xyz, and .itp files of the molecules I am interested in, using Avogadro, ATB, and VMD. I have read the literature of alkaloid molecular dynamic simulations and have the force fields they used to run their simulations. But I cannot for the life of me figure out how to get GROMACS to recognize the residue type.

Do I just add the molecule name to the residuetypes.dat file and name it ALK?

Do I just edit an arbitrary .rtp file in the force field i’m trying to use with the parameters of the molecules i’m having a hard time generating .gro files for?

*gmx pdb2gmx -f mit_all_atom_optimized_geometry.pdb -i mit_all_atom.itp -o mit_all_atom.gro -v *

  •      :-) GROMACS - gmx pdb2gmx, 2022.5-Ubuntu_2022.5_2ubuntu1 (-:*

Executable: /usr/bin/gmx
Data prefix: /usr
Working dir: /home/sigintos/avogadro output
Command line:

  • gmx pdb2gmx -f mit_all_atom_optimized_geometry.pdb -i mit_all_atom.itp -o mit_all_atom.gro -v*

Select the Force Field:

From current directory:

  • 1: CHARMM all-atom force field*

  • 2: CHARMM all-atom force field*

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

  • 4: SIRAH force field 2.2 [Jul 2019]*

From ‘/usr/share/gromacs/top’:

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

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

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

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

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

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

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

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

13: GROMOS96 43a1 force field

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

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

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

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

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

19: 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 mit_all_atom_optimized_geometry.pdb…
WARNING: all CONECT records are ignored
Read ‘ALL ATOM STRUCTURE FOR MOLECULE UNL’, 59 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 1 residues with 59 atoms

  • chain #res #atoms*

  • 1 ’ ’ 1 59 *

Back Off! I just backed up topol.top to ./#topol.top.15#

Processing chain 1 (59 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 2022.5-Ubuntu_2022.5_2ubuntu1
Source file: src/gromacs/gmxpreprocess/resall.cpp (line 617)

Fatal error:
Residue ‘QRV4’ not found in residue topology database

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

Different force field

*gmx pdb2gmx -f mit_all_atom_optimized_geometry.pdb -i mit_all_atom.itp -o mit_all_atom.gro -v
:-) GROMACS - gmx pdb2gmx, 2022.5-Ubuntu_2022.5_2ubuntu1 (-:

Executable: /usr/bin/gmx
Data prefix: /usr
Working dir: /home/sigintos/avogadro output
Command line:
gmx pdb2gmx -f mit_all_atom_optimized_geometry.pdb -i mit_all_atom.itp -o mit_all_atom.gro -v

Select the Force Field:

From current directory:

1: CHARMM all-atom force field

2: CHARMM all-atom force field

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

4: SIRAH force field 2.2 [Jul 2019]

From ‘/usr/share/gromacs/top’:

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

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

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

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

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

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

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

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

13: GROMOS96 43a1 force field

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

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

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

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

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

19: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
3

Using the Gromos54a7_atb force field in directory ./gromos54a7_atb.ff
Opening force field file ./gromos54a7_atb.ff/watermodels.dat

Select the Water Model:

1: SPC simple point charge, recommended

2: SPC/E extended simple point charge

3: None
1

going to rename ./gromos54a7_atb.ff/aminoacids.r2b
Opening force field file ./gromos54a7_atb.ff/aminoacids.r2b
Reading mit_all_atom_optimized_geometry.pdb…
WARNING: all CONECT records are ignored
Read ‘ALL ATOM STRUCTURE FOR MOLECULE UNL’, 59 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 1 residues with 59 atoms

chain #res #atoms

1 ’ ’ 1 59

All occupancies are one
All occupancies are one
Opening force field file ./gromos54a7_atb.ff/atomtypes.atp

Reading residue database… (Gromos54a7_atb)
Opening force field file ./gromos54a7_atb.ff/aminoacids.rtp

Using default: not generating all possible dihedrals

Using default: excluding 3 bonded neighbors

Using default: generating 1,4 H–H interactions

Using default: removing proper dihedrals found on the same bond as a proper dihedral

Using default: removing proper dihedrals found on the same bond as a proper dihedral
Opening force field file ./gromos54a7_atb.ff/aminoacids1.rtp

Using default: not generating all possible dihedrals

Using default: excluding 3 bonded neighbors

Using default: generating 1,4 H–H interactions

Using default: removing proper dihedrals found on the same bond as a proper dihedral

Using default: removing proper dihedrals found on the same bond as a proper dihedral

Program: gmx pdb2gmx, version 2022.5-Ubuntu_2022.5_2ubuntu1
Source file: src/gromacs/gmxpreprocess/resall.cpp (line 469)

Fatal error:
in .rtp file in residue NREXCL at line:
1 HC 1 QRV4 H30 1 0.090 1.0080
*

I have been trying to figure this out for weeks, it is annoying the crap out of me