Editing .hdb file in CHARMM36 force field

GROMACS version:2019
GROMACS modification: No
Here post your question
Dear Gromacs users,
I have several modified/ unnatural nucleotide residues such as 2MG(2-methyl guanosine), 5MC etc. which are present in the .rtp file, and I would want to create a relevant entry for the same such residues. Now my problem is that I am unable to figure out the proper format of .hdb file, of which I have gone through the gromacs manual and understood the basics of it. Although while trying for myself, I have been encountering errors such as:

psg@pslab:~ $ gmx pdb2gmx -f 2MG.pdb -o 2MG.gro -ter
                      :-) GROMACS - gmx pdb2gmx, 2019 (-:

                            GROMACS is written by:
     Emile Apol      Rossen Apostolov      Paul Bauer     Herman J.C. Berendsen
    Par Bjelkmar      Christian Blau   Viacheslav Bolnykh     Kevin Boyd    
 Aldert van Buuren   Rudi van Drunen     Anton Feenstra       Alan Gray     
  Gerrit Groenhof     Anca Hamuraru    Vincent Hindriksen  M. Eric Irrgang  
  Aleksei Iupinov   Christoph Junghans     Joe Jordan     Dimitrios Karkoulis
    Peter Kasson        Jiri Kraus      Carsten Kutzner      Per Larsson    
  Justin A. Lemkul    Viveca Lindahl    Magnus Lundborg     Erik Marklund   
    Pascal Merz     Pieter Meulenhoff    Teemu Murtola       Szilard Pall   
    Sander Pronk      Roland Schulz      Michael Shirts    Alexey Shvetsov  
   Alfons Sijbers     Peter Tieleman      Jon Vincent      Teemu Virolainen 
 Christian Wennberg    Maarten Wolf   
                           and the project leaders:
        Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel

Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2018, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.

GROMACS is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.

GROMACS:      gmx pdb2gmx, version 2019
Executable:   /usr/local/gromacs/bin/gmx
Data prefix:  /usr/local/gromacs
Working dir:  /home/psg/Desktop/Satpati/Ntd/Pal/h_add/final
Command line:
  gmx pdb2gmx -f 2MG.pdb -o 2MG.gro -ter

Select the Force Field:
From current directory:
 1: CHARMM36 all-atom force field (March 2019)
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: CHARMM36 all-atom force field (March 2019)
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)

Using the Charmm36-mar2019 force field in directory ./charmm36-mar2019.ff

Opening force field file ./charmm36-mar2019.ff/watermodels.dat

Select the Water Model:
 1: TIP3P	TIP 3-point, recommended, by default uses CHARMM TIP3 with LJ on H
 2: TIP4P	TIP 4-point
 3: TIP5P	TIP 5-point
 4: SPC		simple point charge
 5: SPC/E	extended simple point charge
 6: None
going to rename ./charmm36-mar2019.ff/merged.r2b
Opening force field file ./charmm36-mar2019.ff/merged.r2b
Reading 2MG.pdb...
Read '', 24 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 24 atoms

  chain  #res #atoms
  1 'A'     1     24  

All occupancies are one
Opening force field file ./charmm36-mar2019.ff/atomtypes.atp
Atomtype 447
Reading residue database... (Charmm36-mar2019)
Opening force field file ./charmm36-mar2019.ff/merged.rtp
Residue 1319
Sorting it all out...
Opening force field file ./charmm36-mar2019.ff/merged.hdb

Program:     gmx pdb2gmx, version 2019
Source file: src/gromacs/gmxpreprocess/h_db.cpp (line 182)

Fatal error:
Error reading from file ./charmm36-mar2019.ff/merged.hdb

I tried editing the .hdb file and it is as follows:

2MG  10
1       6       H5'  C5'  O5'  C4'
1       6       H5'' C5'  C4'  O5'
1       5       H4'  C4'  C5'  O4'      C3'
1       5       H1'  C1'  O4'  N9       C2'
1       1       H8       C8   N9   N7
1       1       H1       N1   C6   C2
1       3       H2       N2   C2   N1
3       4       H21 CM2  N2   C2
3       4       H22 CM2  N2   C2
3       4       H23 CM2  N2   C2
1       5       H3'  C3'  C4'  C2'      O3'
1       6       H2'' C2'  C1'  C3'
1       2       H2'  O2'  C2'  C1'

Attaching the residue herein:

Kindly do point it out where I’m making a mistake in creating the .hdb entry.

Your .hdb entry specifies 10 lines to be read but then you provide 13. You can combine some of them (and should), e.g. for H2[123], which should all be specified as:

3       4       H2 CM2  N2   C2

That should leave you with 11 lines, so you need to have

2MG 11
as the header of this section.

1 Like

Thank you @jalemkul, understood the problem and could do it perfectly.

Hi! I am having a similar issue but cannot understand what is wrong with the hdb parameters. Can you please point out if something is wrong here.
G7M 10
2 6 H5’ C5’ O5’ C4’
1 5 H4’ C4’ C5’ O4’ C3’
1 5 H1’ C1’ O4’ N9 C2’
1 1 H11 C8 N9 N7
1 1 H1 N1 C6 C2
2 3 H2 N2 C2 N1
3 4 H7 CN7 N7 C8
1 5 H3’ C3’ C4’ C2’ O3’
1 5 H2’1 C2’ C1’ C3’ O2’
1 2 HO’2 O2’ C2’ C1’

Thank you!