[gmx-users] pdbgmx warning long bond
maite lopez
lopezmai at gmail.com
Wed Jan 24 15:38:07 CET 2007
Dear Gromacs Users,
I am trying to simulate a peptide in explicit lipid bilayer membrane
environment (say, DPCC). I took well equilibrated dppc.pdb file from
Dr. Peter tieleman site and i modified it put in the names of the
atoms of the ffG53a5.rtp file . I changed DPPC x DPP in ffG53a5.rtp
file. But when executing pdb2gmx ( pdb2gmx_331 -f input.pdb -o
output.gro -p output.top -i output.itp -ffG53a5 -water spc -ignh) i
've gived some errors.
The long bonds are in the atoms of the membrane. Why it could be?
Could anybody give me a pointer to a more elaborated protocol in
setting up and running this type of simulation using gromacs? This is
my first simulation.
This is my output.pdb2gmx_331 file:
Opening library file ffG53a5.rtp
Opening library file aminoacids.dat
Opening library file /usr/local/gromacs331/share/gromacs/top/xlateat.dat
26 out of 26 lines of xlateat.dat converted succesfully
All occupancies are one
Opening library file ffG53a5.atp
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
Opening library file ffG53a5.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 impropers on same bond as a proper
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
Residue 61
Residue 62
Residue 63
Residue 64
Residue 65
Residue 66
Residue 67
Residue 68
Residue 69
Residue 70
Residue 71
Residue 72
Residue 73
Residue 74
Residue 75
Residue 76
Residue 77
Residue 78
Residue 79
Residue 80
Residue 81
Residue 82
Residue 83
Residue 84
Residue 85
Residue 86
Residue 87
Residue 88
Residue 89
Residue 90
Residue 91
Residue 92
Residue 93
Residue 94
Residue 95
Residue 96
Residue 97
Residue 98
Residue 99
Residue 100
Residue 101
Residue 102
Residue 103
Residue 104
Residue 105
Residue 106
Residue 107
Residue 108
Sorting it all out...
Opening library file ffG53a5.hdb
Opening library file /usr/local/gromacs331/share/gromacs/top/ffG53a5-n.tdb
Opening library file /usr/local/gromacs331/share/gromacs/top/ffG53a5-c.tdb
There are 41 donors and 42 acceptors
There are 55 hydrogen bonds
Opening library file /usr/local/gromacs331/share/gromacs/top/specbond.dat
5 out of 5 lines of specbond.dat converted succesfully
Making bonds...
Opening library file aminoacids.dat
Number of bonds was 282, now 277
Generating angles, dihedrals and pairs...
Before cleaning: 477 pairs
Before cleaning: 501 dihedrals
There are 150 dihedrals, 119 impropers, 402 angles
477 pairs, 277 bonds and 0 virtual sites
Total mass 3129.726 a.m.u.
Total charge 1.000 e
Writing topology
There are 64 donors and 0 acceptors
There are 0 hydrogen bonds
Opening library file /usr/local/gromacs331/share/gromacs/top/specbond.dat
5 out of 5 lines of specbond.dat converted succesfully
Making bonds...
Warning: Long Bond (155-156 = 4.66174 nm)
Warning: Long Bond (161-162 = 4.76126 nm)
Warning: Long Bond (198-199 = 4.66509 nm)
Warning: Long Bond (436-437 = 4.20115 nm)
Warning: Long Bond (438-439 = 4.13177 nm)
Warning: Long Bond (439-440 = 4.17203 nm)
Warning: Long Bond (440-441 = 4.14281 nm)
Warning: Long Bond (796-797 = 4.6577 nm)
Warning: Long Bond (855-856 = 4.62827 nm)
Warning: Long Bond (876-877 = 4.71688 nm)
Warning: Long Bond (993-994 = 4.09589 nm)
Warning: Long Bond (1070-1071 = 4.11 nm)
Warning: Long Bond (1094-1095 = 4.10309 nm)
Warning: Long Bond (1113-1132 = 4.15103 nm)
Warning: Long Bond (1134-1136 = 4.59357 nm)
Warning: Long Bond (1141-1142 = 4.59602 nm)
Warning: Long Bond (1163-1182 = 4.59533 nm)
Warning: Long Bond (1171-1172 = 4.57689 nm)
Warning: Long Bond (1224-1225 = 4.68619 nm)
Warning: Long Bond (1230-1231 = 4.59582 nm)
Warning: Long Bond (1384-1386 = 4.17214 nm)
Warning: Long Bond (1386-1387 = 4.13444 nm)
Warning: Long Bond (1387-1388 = 4.15861 nm)
Warning: Long Bond (1388-1389 = 4.14343 nm)
Warning: Long Bond (1389-1390 = 4.14823 nm)
Warning: Long Bond (1390-1391 = 4.16422 nm)
Warning: Long Bond (1391-1392 = 4.13752 nm)
Warning: Long Bond (1392-1393 = 4.17447 nm)
Warning: Long Bond (1393-1394 = 4.13404 nm)
Warning: Long Bond (1399-1400 = 4.08046 nm)
Warning: Long Bond (1445-1446 = 4.12819 nm)
Warning: Long Bond (1446-1447 = 4.17731 nm)
Warning: Long Bond (1465-1467 = 4.66032 nm)
Warning: Long Bond (1467-1468 = 4.64417 nm)
Warning: Long Bond (1468-1469 = 4.64955 nm)
Warning: Long Bond (1473-1474 = 4.65314 nm)
Warning: Long Bond (1474-1475 = 4.6406 nm)
Warning: Long Bond (1475-1476 = 4.65791 nm)
Warning: Long Bond (1476-1477 = 4.69509 nm)
Warning: Long Bond (1477-1478 = 4.6736 nm)
Warning: Long Bond (1478-1479 = 4.65517 nm)
Warning: Long Bond (1480-1481 = 4.6064 nm)
Warning: Long Bond (1495-1496 = 4.64805 nm)
Warning: Long Bond (1627-1628 = 4.09245 nm)
Warning: Long Bond (1648-1649 = 4.15954 nm)
Warning: Long Bond (2028-2029 = 4.16596 nm)
Warning: Long Bond (2128-2129 = 4.575 nm)
Warning: Long Bond (2169-2170 = 4.11031 nm)
Warning: Long Bond (2247-2248 = 4.57523 nm)
Warning: Long Bond (2468-2469 = 4.15575 nm)
Warning: Long Bond (2469-2470 = 4.1968 nm)
Warning: Long Bond (2470-2471 = 4.18024 nm)
Warning: Long Bond (2605-2606 = 4.61836 nm)
Warning: Long Bond (2623-2624 = 4.58482 nm)
Warning: Long Bond (2638-2639 = 4.57666 nm)
Warning: Long Bond (2663-2682 = 6.18936 nm)
Warning: Long Bond (2669-2670 = 4.11224 nm)
Warning: Long Bond (2680-2681 = 4.19622 nm)
Warning: Long Bond (2689-2690 = 4.1131 nm)
Warning: Long Bond (2697-2698 = 4.62574 nm)
Warning: Long Bond (2723-2724 = 4.63025 nm)
Warning: Long Bond (2736-2737 = 4.69821 nm)
Warning: Long Bond (2861-2862 = 4.18192 nm)
Warning: Long Bond (2921-2922 = 4.62338 nm)
Warning: Long Bond (2963-2982 = 4.63017 nm)
Warning: Long Bond (2974-2975 = 4.6299 nm)
Warning: Long Bond (3061-3062 = 4.75158 nm)
Warning: Long Bond (3065-3067 = 4.72777 nm)
Warning: Long Bond (3076-3077 = 4.62963 nm)
Warning: Long Bond (3142-3143 = 4.12151 nm)
Warning: Long Bond (3144-3145 = 4.19034 nm)
Warning: Long Bond (3145-3146 = 4.11515 nm)
Warning: Long Bond (3148-3149 = 4.16624 nm)
Opening library file aminoacids.dat
Number of bonds was 3136, now 3136
Generating angles, dihedrals and pairs...
Before cleaning: 3392 pairs
Before cleaning: 3584 dihedrals
There are 2752 dihedrals, 192 impropers, 3648 angles
3392 pairs, 3136 bonds and 0 virtual sites
Total mass 46979.566 a.m.u.
Total charge -0.000 e
Writing topology
There are 3846 donors and 3846 acceptors
There are 4823 hydrogen bonds
Opening library file /usr/local/gromacs331/share/gromacs/top/specbond.dat
5 out of 5 lines of specbond.dat converted succesfully
Making bonds...
Opening library file aminoacids.dat
Number of bonds was 11538, now 11538
Generating angles, dihedrals and pairs...
There are 0 dihedrals, 0 impropers, 11538 angles
0 pairs, 11538 bonds and 0 virtual sites
Total mass 69287.229 a.m.u.
Total charge 0.000 e
Now there are 15015 atoms and 3940 residues
Total mass in system 119396.520 a.m.u.
Total charge in system 1.000 e
Writing coordinate file...
Reading peptide_dppc64_water.pdb...
Read 'PureDPPC bilayer with 128 lipids and 3655 water molecules and
peptide StII-30', 7266 atoms
Analyzing pdb file
Gave chain 2 chain identifier 'B'
There are 2 chains and 1 blocks of water and 3940 residues with 7266 atoms
chain #res #atoms
1 'A' 30 220
2 'B' 64 3200
3 '-' 3846 3846 (only water)
Reading residue database... (ffG53a5)
Processing chain 1 'A' (220 atoms, 30 residues)
Checking for duplicate atoms....
Now there are 219 atoms. Deleted 1 duplicates.
N-terminus: NH3+
C-terminus: COO-
Now there are 30 residues with 277 atoms
Chain time...
Processing chain 2 'B' (3200 atoms, 64 residues)
Checking for duplicate atoms....
No N- or C-terminus found: this chain appears to contain no protein
Now there are 64 residues with 3200 atoms
Chain time...
Processing chain 3 (3846 atoms, 3846 residues)
Checking for duplicate atoms....
Now there are 3846 residues with 11538 atoms
Including chain 1 in system: 277 atoms 30 residues
Including chain 2 in system: 3200 atoms 64 residues
Including chain 3 in system: 11538 atoms 3846 residues
--------- PLEASE NOTE ------------
You have succesfully generated a topology from: peptide_dppc64_water.pdb.
The G53a5 force field and the spc water model are used.
Note that the default mechanism for selecting a force fields has
changed, starting from GROMACS version 3.2.0
--------- ETON ESAELP ------------
gcq#94: "Once Again Let Me Do This" (Urban Dance Squad)
Cheers,
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