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GMXLIB=“/home/*/gromos54a7.ff” gmx pdb2gmx -f 2k_GSG.pdb -o 1.gro -p 1.top -water spce -merge all -ss yes
:-) GROMACS - gmx pdb2gmx, 2022 (-:
Executable: /usr/local/gromacs/bin/gmx
Data prefix: /usr/local/gromacs
Working dir: /home/*/Desktop/Md_for_hpc_gsh
Command line:
gmx pdb2gmx -f 2k_GSG.pdb -o 1.gro -p 1.top -water spce -merge all -ss yes
Select the Force Field:
From current directory:
1: GROMOS96 54a7 force field (Eur. Biophys. J. (2011), 40, 843-856, DOI: 10.1007/s00249-011-0700-9)
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: GROMOS96 43a1 force field
11: GROMOS96 43a2 force field (improved alkane dihedrals)
12: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
13: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)
14: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
15: GROMOS96 54a7 force field (Eur. Biophys. J. (2011), 40, 843-856, DOI: 10.1007/s00249-011-0700-9)
16: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
1
Using the Gromos54a7 force field in directory ./gromos54a7.ff
going to rename ./gromos54a7.ff/aminoacids.r2b
Opening force field file ./gromos54a7.ff/aminoacids.r2b
Reading 2k_GSG.pdb…
Read ‘’, 3412 atoms
Analyzing pdb file
Splitting chemical chains based on TER records or chain id changing.
Merged chains into joint molecule definitions at 1 places.
There are 1 chains and 0 blocks of water and 415 residues with 3412 atoms
chain #res #atoms
1 ‘A’ 415 3412
there were 0 atoms with zero occupancy and 28 atoms with occupancy unequal to one (out of 3412 atoms). Check your pdb file.
there were 0 atoms with zero occupancy and 28 atoms with occupancy unequal to one (out of 3412 atoms). Check your pdb file.
Opening force field file ./gromos54a7.ff/atomtypes.atp
Reading residue database… (Gromos54a7)
Opening force field file ./gromos54a7.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.ff/aminoacids.hdb
Opening force field file ./gromos54a7.ff/aminoacids.n.tdb
Opening force field file ./gromos54a7.ff/aminoacids.c.tdb
Processing chain 1 ‘A’ (3412 atoms, 415 residues)
Analysing hydrogen-bonding network for automated assignment of histidine
protonation. 661 donors and 635 acceptors were found.
There are 874 hydrogen bonds
Will use HISE for residue 134
Will use HISE for residue 138
Will use HISE for residue 229
Will use HISE for residue 242
Will use HISD for residue 253
Will use HISE for residue 258
Will use HISE for residue 387
Will use HISE for residue 414
Will use HISE for residue 441
Identified residue ASN32 as a starting terminus.
Identified residue SER445 as a ending terminus.
Identified residue GSG1 as a starting terminus.
Identified residue GSG1 as a ending terminus.
1 out of 1 lines of specbond.dat converted successfully
Special Atom Distance matrix:
CYS101 CYS154 CYS177 CYS192 CYS205 CYS251 CYS328
SG575 SG1007 SG1181 SG1297 SG1403 SG1794 SG2400
CYS154 SG1007 2.713
CYS177 SG1181 2.136 2.364
CYS192 SG1297 1.659 1.952 1.563
CYS205 SG1403 2.840 2.362 3.850 2.499
CYS251 SG1794 4.631 3.613 4.275 4.946 5.372
CYS328 SG2400 5.340 5.317 5.937 6.315 6.183 2.685
CYS386 SG2913 4.310 3.483 4.296 4.785 4.973 0.728 2.193
CYS393 SG2969 3.813 3.508 4.239 4.568 4.615 1.617 1.823
CYS411 SG3117 3.955 3.625 3.970 4.611 5.101 1.110 2.156
CYS426 SG3229 2.970 2.164 2.801 3.268 3.864 1.717 3.386
CYS439 SG3333 4.801 4.702 4.719 5.556 6.210 1.672 2.060
GSG1 SG23398 2.827 2.532 3.935 2.561 0.202 5.497 6.237
CYS386 CYS393 CYS411 CYS426 CYS439
SG2913 SG2969 SG3117 SG3229 SG3333
CYS393 SG2969 0.934
CYS411 SG3117 0.834 0.925
CYS426 SG3229 1.539 1.601 1.473
CYS439 SG3333 1.694 1.843 1.140 2.541
GSG1 SG23398 5.083 4.694 5.193 3.979 6.294
Link CYS-205 SG-1403 and GSG-1 SG2-3398 (y/n) ?y
Start terminus ASN-32: NH3+
End terminus SER-445: COO-
Start terminus GSG-1: NH3+
End terminus GSG-1: COO-
WARNING: Duplicate line found in or between hackblock and rtp entries
WARNING: Duplicate line found in or between hackblock and rtp entries
WARNING: Duplicate line found in or between hackblock and rtp entries
WARNING: Duplicate line found in or between hackblock and rtp entries
WARNING: Duplicate line found in or between hackblock and rtp entries
WARNING: Duplicate line found in or between hackblock and rtp entries
WARNING: Duplicate line found in or between hackblock and rtp entries
WARNING: Duplicate line found in or between hackblock and rtp entries
WARNING: Duplicate line found in or between hackblock and rtp entries
WARNING: Duplicate line found in or between hackblock and rtp entries
WARNING: Duplicate line found in or between hackblock and rtp entries
WARNING: Duplicate line found in or between hackblock and rtp entries
WARNING: Duplicate line found in or between hackblock and rtp entries
WARNING: Duplicate line found in or between hackblock and rtp entries
WARNING: Duplicate line found in or between hackblock and rtp entries
WARNING: Duplicate line found in or between hackblock and rtp entries
WARNING: Duplicate line found in or between hackblock and rtp entries
WARNING: Duplicate line found in or between hackblock and rtp entries
WARNING: Duplicate line found in or between hackblock and rtp entries
WARNING: Duplicate line found in or between hackblock and rtp entries
Program: gmx pdb2gmx, version 2022
Source file: src/gromacs/gmxpreprocess/pdb2top.cpp (line 1132)
Fatal error:
atom N not found in buiding block 415GSG2 while combining tdb and rtp
For more information and tips for troubleshooting, please check the GROMACS
website at Common Errors — GROMACS webpage https://www.gromacs.org documentation
Hi, I am attempting to run MD on a protein that has undergone S-Glutathionylation and I do not understand the error that I am receiving. I believe my pdb and gromos 54a7ff have both been adequately modified to incorporate the s-glutathionylation. Where could this error be coming from? Why does it refer to an error in building block 415GSG2 when this is not present in the PDB?
From PDB:
ATOM 3570 OG SER A 445 -45.318 72.708 -2.486 1.00 97.85 O
ANISOU 3570 OG SER A 445 12561 12991 11628 1377 -1030 -950 O
ATOM 1 O32 GSG 1 13.363 61.097 0.853 1.00 0.00 O
ATOM 2 C3 GSG 1 13.562 60.873 2.071 1.00 0.00 C
ATOM 3 O31 GSG 1 12.845 61.217 3.054 1.00 0.00 O
ATOM 4 CA3 GSG 1 14.869 60.098 2.401 1.00 0.00 C
ATOM 7 N3 GSG 1 14.898 59.752 3.811 1.00 0.00 N
ATOM 8 H3 GSG 1 14.120 60.170 4.317 1.00 0.00 H
ATOM 9 C2 GSG 1 15.643 58.752 4.329 1.00 0.00 C
ATOM 10 O2 GSG 1 16.494 58.141 3.676 1.00 0.00 O
ATOM 11 CA2 GSG 1 15.312 58.402 5.806 1.00 0.00 C
ATOM 13 CB2 GSG 1 15.489 59.598 6.776 1.00 0.00 C
ATOM 14 SG2 GSG 1 14.977 59.248 8.520 1.00 0.00 S
ATOM 18 N2 GSG 1 16.036 57.206 6.217 1.00 0.00 N
ATOM 19 H2 GSG 1 15.486 56.368 6.340 1.00 0.00 H
ATOM 20 CD1 GSG 1 17.348 57.127 6.513 1.00 0.00 C
ATOM 21 OE1 GSG 1 18.139 58.082 6.419 1.00 0.00 O
ATOM 22 CG1 GSG 1 17.813 55.778 7.060 1.00 0.00 C
ATOM 25 CB1 GSG 1 18.648 55.929 8.345 1.00 0.00 C
ATOM 28 CA1 GSG 1 17.949 56.648 9.504 1.00 0.00 C
ATOM 30 C1 GSG 1 18.678 56.435 10.879 1.00 0.00 C
ATOM 31 O11 GSG 1 18.885 55.249 11.213 1.00 0.00 O
ATOM 32 O12 GSG 1 18.959 57.492 11.516 1.00 0.00 O
ATOM 33 N1 GSG 1 17.852 58.135 9.285 1.00 0.00 N
ATOM 34 H11 GSG 1 16.850 58.489 9.141 1.00 0.00 H
ATOM 35 H12 GSG 1 18.279 58.527 10.152 1.00 0.00 H
ATOM 36 H13 GSG 1 18.376 58.428 8.451 1.00 0.00 H
END