[gmx-users] pdbgmx warning long bond
Tsjerk Wassenaar
tsjerkw at gmail.com
Thu Jan 25 11:14:36 CET 2007
Greg,
This likely does not reflect Maites problem. There was no mention of
editing a pdb file to get the names right. Maite is dealing with
lipids/protein, whereas you're dealing with DNA. That's a completely
different topic, with particular problems, like the one you mention.
Tsjerk
On 1/25/07, Gregoire Masliah <masliah at igr.fr> wrote:
> 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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--
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
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