[gmx-users] Too many error at first step

Mon Jan 30 17:09:20 CET 2017

Hello all,

I am new to Gromacs, and I completed the Lysozyme tutorial. But When I
started stimulation with my own protein, I got many errors. I am not
understanding what to do?

For error
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lab at lab-desktop:~/Desktop/MD_tutorial$ gmx pdb2gmx -f 4g7a.pdb -o
4g7a_processed.gro -water spce
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gmx pdb2gmx -f 4g7a.pdb -o 4g7a_processed.gro -water spce

Select the Force Field:
>From '/usr/local/gromacs/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)
15

Using the Oplsaa force field in directory oplsaa.ff

Opening force field file
/usr/local/gromacs/share/gromacs/top/oplsaa.ff/aminoacids.r2b
Reading 4g7a.pdb...

*WARNING: all CONECT records are ignored*
Read 'CARBONATE DEHYDRATASE', 3726 atoms
Analyzing pdb file
Splitting chemical chains based on TER records or chain id changing.

*WARNING: Chain identifier 'A' is used in two non-sequential blocks*.
They will be treated as separate chains unless you reorder your file.

*WARNING: Chain identifier 'B' is used in two non-sequential blocks.*
They will be treated as separate chains unless you reorder your file.
There are 4 chains and 0 blocks of water and 453 residues with 3726 atoms

chain #res <https://plus.google.com/u/0/s/%23res> #atoms
<https://plus.google.com/u/0/s/%23atoms>
1 'A' 224 1850
2 'B' 225 1848
3 'A' 2 14
4 'B' 2 14

*WARNING: there were 0 atoms with zero occupancy and 24 atoms withoccupancy
unequal to one (out of 3726 atoms). Check your pdb file.*

Opening force field file
/usr/local/gromacs/share/gromacs/top/oplsaa.ff/atomtypes.atp
Atomtype 814
Reading residue database... (oplsaa)
Opening force field file
/usr/local/gromacs/share/gromacs/top/oplsaa.ff/aminoacids.rtp
Residue 51
Sorting it all out...
Opening force field file
/usr/local/gromacs/share/gromacs/top/oplsaa.ff/aminoacids.hdb
Opening force field file
/usr/local/gromacs/share/gromacs/top/oplsaa.ff/aminoacids.n.tdb
Opening force field file
/usr/local/gromacs/share/gromacs/top/oplsaa.ff/aminoacids.c.tdb
Processing chain 1 'A' (1850 atoms, 224 residues)
Analysing hydrogen-bonding network for automated assignment of histidine
protonation. 348 donors and 340 acceptors were found.
There are 571 hydrogen bonds
Will use HISE for residue 13
Will use HISE for residue 64
Will use HISD for residue 89
Will use HISD for residue 91
Will use HISH for residue 96
Will use HISE for residue 108
Will use HISE for residue 111
Identified residue GLU2 as a starting terminus.
Identified residue PHE225 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Special Atom Distance matrix:
HIS13 CYS24 HIS64 HIS89 HIS91 HIS96 HIS108
NE2102 SG205 NE2537 NE2752 NE2773 NE2812 NE2920
CYS24 SG205 1.292
HIS64 NE2537 1.662 1.215
HIS89 NE2752 2.291 1.422 1.134
HIS91 NE2773 2.078 1.340 1.109 0.319
HIS96 NE2812 2.309 1.478 1.921 1.078 0.956
HIS108 NE2920 2.341 1.518 1.551 0.549 0.461 0.594
HIS111 NE2948 3.366 2.266 2.218 1.186 1.430 1.481 1.207
MET124 SD1042 2.668 2.087 2.115 1.201 1.040 0.821 0.722
MET167 SD1384 3.105 2.374 2.793 1.822 1.730 0.920 1.288
CYS178 SG1462 1.405 0.204 1.183 1.243 1.160 1.286 1.317
MET205 SD1680 2.313 1.909 1.145 0.868 0.772 1.646 1.112
HIS111 MET124 MET167 CYS178
NE2948 SD1042 SD1384 SG1462
MET124 SD1042 1.600
MET167 SD1384 1.756 0.956
CYS178 SG1462 2.083 1.895 2.189
MET205 SD1680 1.859 1.368 2.264 1.770
Linking CYS-24 SG-205 and CYS-178 SG-1462...
Start terminus GLU-2: NH3+
End terminus PHE-225: COO-
Checking for duplicate atoms....
Now there are 1838 atoms. Deleted 12 duplicates.
Generating any missing hydrogen atoms and/or adding termini.
Now there are 224 residues with 3714 atoms
Chain time...
Making bonds...
Number of bonds was 3759, now 3759
Generating angles, dihedrals and pairs...
Before cleaning: 9973 pairs
Before cleaning: 10098 dihedrals
Keeping all generated dihedrals
Making cmap torsions...
There are 10098 dihedrals, 698 impropers, 6858 angles
9913 pairs, 3759 bonds and 0 virtual sites
Total mass 26036.211 a.m.u.
Total charge 8.548 e
Writing topology
Processing chain 2 'B' (1848 atoms, 225 residues)
Analysing hydrogen-bonding network for automated assignment of histidine
protonation. 347 donors and 337 acceptors were found.
There are 552 hydrogen bonds
Will use HISE for residue 1
Will use HISE for residue 13
Will use HISE for residue 64
Will use HISD for residue 89
Will use HISD for residue 91
Will use HISH for residue 96
Will use HISE for residue 108
Will use HISH for residue 111
Identified residue HIS1 as a starting terminus.
Identified residue PHE225 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Special Atom Distance matrix:
HIS1 HIS13 CYS24 HIS64 HIS89 HIS91 HIS96
NE210 NE2112 SG215 NE2541 NE2756 NE2777 NE2816
HIS13 NE2112 1.745
CYS24 SG215 1.666 1.257
HIS64 NE2541 0.500 1.577 1.214
HIS89 NE2756 1.514 2.190 1.415 1.130
HIS91 NE2777 1.489 1.982 1.344 1.115 0.315
HIS96 NE2816 2.357 2.227 1.484 1.924 1.081 0.956
HIS108 NE2918 1.946 2.252 1.526 1.555 0.551 0.459 0.601
HIS111 NE2946 2.566 3.262 2.242 2.196 1.172 1.412 1.483
MET124 SD1040 2.434 2.585 2.097 2.116 1.194 1.033 0.823
MET167 SD1382 3.228 3.066 2.419 2.830 1.853 1.758 0.958
CYS178 SG1460 1.659 1.358 0.203 1.185 1.238 1.166 1.291
MET205 SD1678 1.254 2.207 1.915 1.146 0.874 0.778 1.653
HIS108 HIS111 MET124 MET167 CYS178
NE2918 NE2946 SD1040 SD1382 SG1460
HIS111 NE2946 1.196
MET124 SD1040 0.711 1.581
MET167 SD1382 1.317 1.779 0.974
CYS178 SG1460 1.326 2.060 1.905 2.233
MET205 SD1678 1.116 1.849 1.369 2.293 1.779
Linking CYS-24 SG-215 and CYS-178 SG-1460...
Start terminus HIS-1: NH3+
End terminus PHE-225: COO-
Checking for duplicate atoms....
Generating any missing hydrogen atoms and/or adding termini.
Now there are 225 residues with 3732 atoms
Chain time...
Making bonds...
Number of bonds was 3778, now 3778
Generating angles, dihedrals and pairs...
Before cleaning: 10019 pairs
Before cleaning: 10149 dihedrals
Keeping all generated dihedrals
Making cmap torsions...
There are 10149 dihedrals, 705 impropers, 6891 angles
9959 pairs, 3778 bonds and 0 virtual sites
Total mass 26174.361 a.m.u.
Total charge 9.548 e
Writing topology
Processing chain 3 'A' (14 atoms, 2 residues)
Warning: Starting residue ZN301 in chain not identified as Protein/RNA/DNA.
Warning: Starting residue AZM302 in chain not identified as Protein/RNA/DNA.
Problem with chain definition, or missing terminal residues.
This chain does not appear to contain a recognized chain molecule.
If this is incorrect, you can edit residuetypes.dat to modify the behavior.
8 out of 8 lines of specbond.dat converted successfully

-------------------------------------------------------
Program gmx pdb2gmx, VERSION 5.1.4
Source code file:
/home/lab/gromacs-5.1.4/src/gromacs/gmxpreprocess/resall.c, line: 645

*Fatal error:Residue 'ZN' not found in residue topology database*
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
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lab at lab-desktop:~/Desktop/MD_tutorial$

-- 
Regards,
Chintan Bhagat
Mob. +91 88 66 61 11 49

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