[gmx-users] pdbgmx warning long bond
Gregoire Masliah
masliah at igr.fr
Thu Jan 25 09:40:41 CET 2007
I had the same problem few days ago (this was my first simulation too ;)
when running a simulation on a standard B-DNA.
I modified the names of atoms and residus in the pdb file of my dna to
match G43a1.rtp names. Then when I run pdb2gmx I had the same warning.
I tried to open the modified pdb file in say rasmol, and I saw that the
molecule was totally modified as well.
Explanation: when modifying the name of residus name (this apply to
atoms as well), I had modified the strict columns format of the pdb
file. Then the 3 fields corresponding to xyz coordinates were shifted by
a few number of columns and from that, misinterpreted by the pdb2gmx.
Knowing that the fix is straightforward.
Hope this can help
Greg
maite lopez wrote:
> 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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