I have converted a .cif file into .pdb file (myfile.txt, attached here) using openbabel
commandline: obabel -i cif myfile.cif -o pdb -O myfile.pdb
myfile.txt (171.6 KB)
But after this, pdb2gmx conversion in gromacs is not running. I want to use AMBER99SB protein, nucleic AMBER94 or AMBER99SB-ILDN protein, nucleic AMBER94. Please help!
Error:
$ gmx pdb2gmx -f start_clean.pdb -o complex.gro -ignh
:-) GROMACS - gmx pdb2gmx, 2021.4-Ubuntu-2021.4-2 (-:
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GROMACS: gmx pdb2gmx, version 2021.4-Ubuntu-2021.4-2
Executable: /usr/bin/gmx
Data prefix: /usr
Working dir: /media/soumya/HD1/ParamShakti/SCR/AF3_july1/3m-dna
Command line:
gmx pdb2gmx -f start_clean.pdb -o complex.gro -ignh
Select the Force Field:
From ‘/usr/share/gromacs/top’:
1: AMBER03 protein, nucleic AMBER94 (Duan et al., J. Comp. Chem. 24, 1999-2012, 2003)
2: AMBER94 force field (Cornell et al., JACS 117, 5179-5197, 1995)
3: AMBER96 protein, nucleic AMBER94 (Kollman et al., Acc. Chem. Res. 29, 461-469, 1996)
4: AMBER99 protein, nucleic AMBER94 (Wang et al., J. Comp. Chem. 21, 1049-1074, 2000)
5: AMBER99SB protein, nucleic AMBER94 (Hornak et al., Proteins 65, 712-725, 2006)
6: AMBER99SB-ILDN protein, nucleic AMBER94 (Lindorff-Larsen et al., Proteins 78, 1950-58, 2010)
7: AMBERGS force field (Garcia & Sanbonmatsu, PNAS 99, 2782-2787, 2002)
8: CHARMM27 all-atom force field (CHARM22 plus CMAP for proteins)
9: GROMOS96 43a1 force field
10: GROMOS96 43a2 force field (improved alkane dihedrals)
11: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
12: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)
13: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
14: GROMOS96 54a7 force field (Eur. Biophys. J. (2011), 40, 843-856, DOI: 10.1007/s00249-011-0700-9)
15: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
6
Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
Opening force field file /usr/share/gromacs/top/amber99sb-ildn.ff/watermodels.dat
Select the Water Model:
1: TIP3P TIP 3-point, recommended
2: TIP4P TIP 4-point
3: TIP4P-Ew TIP 4-point optimized with Ewald
4: TIP5P TIP 5-point (see OPLS/AA not compatible with TIP5P - Redmine #1348 (#1348) · Issues · GROMACS / GROMACS · GitLab for issues)
5: SPC simple point charge
6: SPC/E extended simple point charge
7: None
1
going to rename amber99sb-ildn.ff/aminoacids.r2b
Opening force field file /usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.r2b
going to rename amber99sb-ildn.ff/dna.r2b
Opening force field file /usr/share/gromacs/top/amber99sb-ildn.ff/dna.r2b
going to rename amber99sb-ildn.ff/rna.r2b
Opening force field file /usr/share/gromacs/top/amber99sb-ildn.ff/rna.r2b
Reading start_clean.pdb…
WARNING: all CONECT records are ignored
Read '5fbbe3dda33eebc1 ', 1142 atoms
Analyzing pdb file
Splitting chemical chains based on TER records or chain id changing.
There are 3 chains and 0 blocks of water and 89 residues with 1142 atoms
chain #res #atoms
1 ‘A’ 61 566
2 ‘B’ 14 291
3 ‘C’ 14 285
All occupancies are one
All occupancies are one
Opening force field file /usr/share/gromacs/top/amber99sb-ildn.ff/atomtypes.atp
Reading residue database… (Amber99sb-ildn)
Opening force field file /usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.rtp
Opening force field file /usr/share/gromacs/top/amber99sb-ildn.ff/dna.rtp
Opening force field file /usr/share/gromacs/top/amber99sb-ildn.ff/rna.rtp
Opening force field file /usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.hdb
Opening force field file /usr/share/gromacs/top/amber99sb-ildn.ff/dna.hdb
Opening force field file /usr/share/gromacs/top/amber99sb-ildn.ff/rna.hdb
Opening force field file /usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.n.tdb
Opening force field file /usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.c.tdb
Back Off! I just backed up topol.top to ./#topol.top.1#
Processing chain 1 ‘A’ (566 atoms, 61 residues)
Analysing hydrogen-bonding network for automated assignment of histidine
protonation. 126 donors and 93 acceptors were found.
There are 118 hydrogen bonds
Will use HISE for residue 21
Will use HISD for residue 60
Identified residue THR1 as a starting terminus.
Identified residue LYS61 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Special Atom Distance matrix:
HIS21 MET54
NE2191 SD495
MET54 SD495 2.081
HIS60 NE2556 1.197 1.389
Opening force field file /usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.arn
Opening force field file /usr/share/gromacs/top/amber99sb-ildn.ff/dna.arn
Opening force field file /usr/share/gromacs/top/amber99sb-ildn.ff/rna.arn
Checking for duplicate atoms…
Generating any missing hydrogen atoms and/or adding termini.
Now there are 61 residues with 1147 atoms
Chain time…
Back Off! I just backed up topol_Protein_chain_A.itp to ./#topol_Protein_chain_A.itp.1#
Making bonds…
Number of bonds was 1159, now 1158
Generating angles, dihedrals and pairs…
Before cleaning: 3023 pairs
Before cleaning: 3076 dihedrals
Keeping all generated dihedrals
Making cmap torsions…
There are 3076 dihedrals, 247 impropers, 2074 angles
2999 pairs, 1158 bonds and 0 virtual sites
Total mass 8010.418 a.m.u.
Total charge 11.000 e
Writing topology
Back Off! I just backed up posre_Protein_chain_A.itp to ./#posre_Protein_chain_A.itp.1#
Processing chain 2 ‘B’ (291 atoms, 14 residues)
Identified residue DA1 as a starting terminus.
Identified residue DG14 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Opening force field file /usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.arn
Opening force field file /usr/share/gromacs/top/amber99sb-ildn.ff/dna.arn
Opening force field file /usr/share/gromacs/top/amber99sb-ildn.ff/rna.arn
Program: gmx pdb2gmx, version 2021.4-Ubuntu-2021.4-2
Source file: src/gromacs/gmxpreprocess/pdb2gmx.cpp (line 790)
Fatal error:
Atom OP3 in residue DA 1 was not found in rtp entry DA5 with 30 atoms
while sorting atoms.
.