GROMACS version:2019
GROMACS modification: No
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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 (-:
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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)
1
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
1
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.
Regards,
Pallav
