hello：
This is my screen outputs. I have tried many times but it seems that the reason is TRP CH2 cannot be read? how can i change the name of TRP? just change the"TRP" to another amino acid name? how can i fix this bug? thank you!
Select the Force Field:
From current directory:
1: CHARMM all-atom force field
From ‘/home/z/Downloads/GMX/2023-CPU2/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 Charmm36_ljpme-jul2022 force field in directory ./charmm36_ljpme-jul2022.ff
Opening force field file ./charmm36_ljpme-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_ljpme-jul2022.ff/aminoacids.r2b
Opening force field file ./charmm36_ljpme-jul2022.ff/aminoacids.r2b
going to rename ./charmm36_ljpme-jul2022.ff/carb.r2b
Opening force field file ./charmm36_ljpme-jul2022.ff/carb.r2b
going to rename ./charmm36_ljpme-jul2022.ff/cgenff.r2b
Opening force field file ./charmm36_ljpme-jul2022.ff/cgenff.r2b
going to rename ./charmm36_ljpme-jul2022.ff/ethers.r2b
Opening force field file ./charmm36_ljpme-jul2022.ff/ethers.r2b
going to rename ./charmm36_ljpme-jul2022.ff/lipid.r2b
Opening force field file ./charmm36_ljpme-jul2022.ff/lipid.r2b
going to rename ./charmm36_ljpme-jul2022.ff/metals.r2b
Opening force field file ./charmm36_ljpme-jul2022.ff/metals.r2b
going to rename ./charmm36_ljpme-jul2022.ff/na.r2b
Opening force field file ./charmm36_ljpme-jul2022.ff/na.r2b
going to rename ./charmm36_ljpme-jul2022.ff/silicates.r2b
Opening force field file ./charmm36_ljpme-jul2022.ff/silicates.r2b
going to rename ./charmm36_ljpme-jul2022.ff/solvent.r2b
Opening force field file ./charmm36_ljpme-jul2022.ff/solvent.r2b
Reading bestP34.pdb…
Read ‘’, 2884 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 370 residues with 2884 atoms
chain #res #atoms
1 ‘A’ 370 2884
All occupancies are one
All occupancies are one
Opening force field file ./charmm36_ljpme-jul2022.ff/atomtypes.atp
Reading residue database… (Charmm36_ljpme-jul2022)
Opening force field file ./charmm36_ljpme-jul2022.ff/aminoacids.rtp
Opening force field file ./charmm36_ljpme-jul2022.ff/carb.rtp
Opening force field file ./charmm36_ljpme-jul2022.ff/cgenff.rtp
Opening force field file ./charmm36_ljpme-jul2022.ff/ethers.rtp
Opening force field file ./charmm36_ljpme-jul2022.ff/lipid.rtp
Opening force field file ./charmm36_ljpme-jul2022.ff/metals.rtp
Opening force field file ./charmm36_ljpme-jul2022.ff/na.rtp
Opening force field file ./charmm36_ljpme-jul2022.ff/silicates.rtp
Opening force field file ./charmm36_ljpme-jul2022.ff/solvent.rtp
Opening force field file ./charmm36_ljpme-jul2022.ff/aminoacids.hdb
Opening force field file ./charmm36_ljpme-jul2022.ff/carb.hdb
Opening force field file ./charmm36_ljpme-jul2022.ff/cgenff.hdb
Opening force field file ./charmm36_ljpme-jul2022.ff/ethers.hdb
Opening force field file ./charmm36_ljpme-jul2022.ff/lipid.hdb
Opening force field file ./charmm36_ljpme-jul2022.ff/metals.hdb
Opening force field file ./charmm36_ljpme-jul2022.ff/na.hdb
Opening force field file ./charmm36_ljpme-jul2022.ff/silicates.hdb
Opening force field file ./charmm36_ljpme-jul2022.ff/solvent.hdb
Opening force field file ./charmm36_ljpme-jul2022.ff/aminoacids.n.tdb
Opening force field file ./charmm36_ljpme-jul2022.ff/carb.n.tdb
Opening force field file ./charmm36_ljpme-jul2022.ff/cgenff.n.tdb
Opening force field file ./charmm36_ljpme-jul2022.ff/ethers.n.tdb
Opening force field file ./charmm36_ljpme-jul2022.ff/lipid.n.tdb
Opening force field file ./charmm36_ljpme-jul2022.ff/metals.n.tdb
Opening force field file ./charmm36_ljpme-jul2022.ff/na.n.tdb
Opening force field file ./charmm36_ljpme-jul2022.ff/silicates.n.tdb
Opening force field file ./charmm36_ljpme-jul2022.ff/solvent.n.tdb
Opening force field file ./charmm36_ljpme-jul2022.ff/aminoacids.c.tdb
Opening force field file ./charmm36_ljpme-jul2022.ff/carb.c.tdb
Opening force field file ./charmm36_ljpme-jul2022.ff/cgenff.c.tdb
Opening force field file ./charmm36_ljpme-jul2022.ff/ethers.c.tdb
Opening force field file ./charmm36_ljpme-jul2022.ff/lipid.c.tdb
Opening force field file ./charmm36_ljpme-jul2022.ff/metals.c.tdb
Opening force field file ./charmm36_ljpme-jul2022.ff/na.c.tdb
Opening force field file ./charmm36_ljpme-jul2022.ff/silicates.c.tdb
Opening force field file ./charmm36_ljpme-jul2022.ff/solvent.c.tdb
Processing chain 1 ‘A’ (2884 atoms, 370 residues)
Analysing hydrogen-bonding network for automated assignment of histidine
protonation. 528 donors and 554 acceptors were found.
There are 823 hydrogen bonds
Will use HISE for residue 23
Will use HISE for residue 51
Will use HISD for residue 56
Will use HISE for residue 58
Will use HISD for residue 86
Will use HISE for residue 88
Will use HISE for residue 125
Will use HISE for residue 163
Will use HISE for residue 203
Will use HISE for residue 272
Will use HISE for residue 292
Will use HISE for residue 362
Will use HISE for residue 367
Identified residue MET1 as a starting terminus.
Identified residue LEU370 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Special Atom Distance matrix:
MET1 HIS23 HIS51 HIS56 HIS58 MET78 HIS86
SD7 NE2168 NE2401 NE2442 NE2460 SD628 NE2691
HIS23 NE2168 4.310
HIS51 NE2401 4.908 0.919
HIS56 NE2442 6.019 2.742 1.929
HIS58 NE2460 6.724 3.389 2.475 1.410
MET78 SD628 6.462 2.215 1.992 3.173 3.286
HIS86 NE2691 6.517 2.336 2.285 3.546 3.759 0.499
HIS88 NE2707 6.039 1.832 1.847 3.220 3.594 0.679 0.549
MET120 SD964 6.917 3.813 4.186 5.105 6.009 3.547 3.163
CYS123 SG984 6.043 3.462 4.047 5.240 6.183 3.722 3.345
HIS125 NE21002 6.468 3.983 4.597 5.900 6.751 4.025 3.591
CYS147 SG1173 5.858 2.426 2.038 1.662 2.936 2.940 3.101
HIS163 NE21283 4.894 3.045 3.477 4.091 5.372 4.295 4.176
CYS181 SG1411 6.159 3.499 3.411 3.063 4.416 4.188 4.208
HIS203 NE21599 6.636 3.966 3.949 3.711 5.015 4.451 4.399
CYS221 SG1731 6.304 3.691 3.578 3.133 4.487 4.354 4.381
MET240 SD1880 6.923 3.296 3.481 4.277 5.087 2.688 2.355
HIS272 NE22128 6.256 2.028 1.658 2.316 2.918 1.308 1.462
CYS284 SG2216 6.587 2.418 2.351 3.282 3.807 1.209 1.005
HIS292 NE22277 5.800 1.862 1.775 2.488 3.420 1.973 1.982
CYS337 SG2627 6.483 2.369 2.381 3.390 3.955 1.308 1.050
MET339 SD2638 6.085 2.328 2.545 3.540 4.373 2.096 1.846
HIS362 NE22819 6.445 5.471 6.039 6.740 8.008 6.378 6.098
HIS367 NE22862 6.637 5.923 6.624 7.649 8.811 6.746 6.396
HIS88 MET120 CYS123 HIS125 CYS147 HIS163 CYS181
NE2707 SD964 SG984 NE21002 SG1173 NE21283 SG1411
MET120 SD964 3.001
CYS123 SG984 3.082 1.086
HIS125 NE21002 3.425 1.403 0.797
CYS147 SG1173 2.688 3.637 3.824 4.541
HIS163 NE21283 3.690 2.842 2.455 3.226 2.641
CYS181 SG1411 3.791 3.440 3.646 4.422 1.565 1.955
HIS203 NE21599 4.025 3.101 3.427 4.170 2.142 2.029 0.748
CYS221 SG1731 3.972 3.589 3.820 4.593 1.688 2.114 0.209
MET240 SD1880 2.221 1.035 1.796 2.199 2.926 2.958 3.078
HIS272 NE22128 1.167 3.129 3.404 3.923 1.683 3.383 2.926
CYS284 SG2216 0.896 2.459 2.829 3.215 2.441 3.495 3.349
HIS292 NE22277 1.546 2.647 2.816 3.446 1.303 2.517 2.247
CYS337 SG2627 0.895 2.295 2.630 3.015 2.484 3.369 3.329
MET339 SD2638 1.521 1.680 1.910 2.456 2.284 2.535 2.760
HIS362 NE22819 5.728 3.414 2.989 3.343 5.167 2.716 4.083
HIS367 NE22862 6.081 3.713 3.078 3.090 6.126 3.682 5.284
HIS203 CYS221 MET240 HIS272 CYS284 HIS292 CYS337
NE21599 SG1731 SD1880 NE22128 SG2216 NE22277 SG2627
CYS221 SG1731 0.736
MET240 SD1880 2.871 3.230
HIS272 NE22128 3.228 3.081 2.198
CYS284 SG2216 3.463 3.513 1.519 0.966
HIS292 NE22277 2.536 2.427 1.873 0.870 1.268
CYS337 SG2627 3.426 3.499 1.392 1.087 0.208 1.255
MET339 SD2638 2.790 2.944 0.973 1.512 1.060 1.060 0.897
HIS362 NE22819 3.676 4.161 4.199 5.645 5.391 4.824 5.224
HIS367 NE22862 4.911 5.394 4.656 6.273 5.850 5.520 5.658
MET339 HIS362
SD2638 NE22819
HIS362 NE22819 4.340
HIS367 NE22862 4.839 1.491
Linking CYS-181 SG-1411 and CYS-221 SG-1731…
Linking CYS-284 SG-2216 and CYS-337 SG-2627…
Select start terminus type for MET-1
0: MET1
1: NH3+
2: NH2
3: HYD1
4: 5TER
5: 5MET
6: 5PHO
7: 5POM
8: None
2
Start terminus MET-1: NH2
Select end terminus type for LEU-370
0: COO-
1: COOH
2: CT2
3: CT1
4: HYD2
5: MET2
6: 3TER
7: None
1
End terminus LEU-370: COOH
Opening force field file ./charmm36_ljpme-jul2022.ff/aminoacids.arn
Checking for duplicate atoms…
Generating any missing hydrogen atoms and/or adding termini.
Program: gmx pdb2gmx, version 2023
Source file: src/gromacs/gmxpreprocess/pgutil.cpp (line 154)
Fatal error:
Residue 47 named TRP of a molecule in the input file was mapped
to an entry in the topology database, but the atom CH2 used in
that entry is not found in the input file. Perhaps your atom
and/or residue naming needs to be fixed.
For more information and tips for troubleshooting, please check the GROMACS
website at Common Errors — GROMACS webpage https://www.gromacs.org documentation