[gmx-users] problem by start with grompp
Justin Lemkul
jalemkul at vt.edu
Thu Jan 3 13:39:18 CET 2013
On 1/3/13 7:34 AM, Alexej Mazheika wrote:
> Dear all!
>
> I'm new with Gromacs.
> I prepared some job for it but I cann't start with grompp. It writes me
> "Fatal error:
> Something is wrong in the coordinate formatting of file conf.gro. Note that
> gro is fixed format (see the manual)".
> What is wrong? I want to calculate a silver cluster contining 125 atoms.
> And the conf.gro file was prepared according to on-line manual of Gromacs.
> Input-files (conf.gro, topol.top and silver.itp) are shown below.
>
> Thank you in advance,
> Alex
>
> *conf.gro:*
>
> Bulk silver, t = 0.0
> 125
> Cluster Ag 1 0.000 0.000 0.000 0.3549 0.4758
> -0.0904
Immediately you can see that the format is wrong. First comes a residue number
(5 characters, right-aligned), then a residue name (also 5 characters max).
Your file satisfies neither requirement, as you have no residue number and a
7-character residue name. Email format makes it somewhat hard to judge the
remainder of the file, but at a glance, it appears the spacing is misaligned for
all columns. Refer again to the online manual and compare your format against
existing examples (like spc216.gro in $GMXLIB).
-Justin
> Cluster Ag 2 0.204 0.204 0.000 0.5023 0.6171
> -0.1193
> Cluster Ag 3 0.409 0.409 0.000 0.1706 1.9242
> -0.1299
> Cluster Ag 4 -0.409 -0.409 0.000 0.1853 -0.0977
> 0.2463
> Cluster Ag 5 -0.204 -0.204 0.000 -0.1168
> -0.0371 0.9161
> Cluster Ag 6 0.204 0.000 0.204 -0.0551 1.4850
> -0.1296
> Cluster Ag 7 0.409 0.204 0.204 0.3101 -0.3484
> -0.0008
> Cluster Ag 8 0.613 0.409 0.204 0.5298 0.4809
> 0.2331
> Cluster Ag 9 -0.204 -0.409 0.204 -0.4401
> -0.3946 1.5223
> Cluster Ag 10 0.000 -0.204 0.204 -0.0845
> -0.0352 -0.6628
> Cluster Ag 11 0.409 0.000 0.409 -0.5423 0.5471
> -0.3902
> Cluster Ag 12 0.613 0.204 0.409 -3.1280 0.3170
> -1.0229
> Cluster Ag 13 0.817 0.409 0.409 0.6789 0.0640
> -0.0344
> Cluster Ag 14 0.000 -0.409 0.409 -0.1302 0.1578
> -0.0127
> Cluster Ag 15 0.204 -0.204 0.409 0.6698 1.0679
> -1.3227
> Cluster Ag 16 -0.409 0.000 -0.409 -0.2256
> -0.3632 0.0514
> Cluster Ag 17 -0.204 0.204 -0.409 0.2069
> -0.2388 0.6106
> Cluster Ag 18 0.000 0.409 -0.409 0.7349 1.3763
> -0.9274
> Cluster Ag 19 -0.817 -0.409 -0.409 -0.9525
> -0.2627 0.4172
> Cluster Ag 20 -0.613 -0.204 -0.409 0.5542
> -0.4907 -0.0019
> Cluster Ag 21 -0.204 0.000 -0.204 1.2732 1.4340
> -0.3768
> Cluster Ag 22 0.000 0.204 -0.204 0.0591 -0.1353
> -0.5894
> Cluster Ag 23 0.204 0.409 -0.204 -0.5937
> -0.1721 0.0862
> Cluster Ag 24 -0.613 -0.409 -0.204 0.4257
> 2.1061 0.2350
> Cluster Ag 25 -0.409 -0.204 -0.204 0.2298
> -0.0775 0.3642
> Cluster Ag 26 0.000 0.204 0.204 -0.0384 0.0506
> -0.0643
> Cluster Ag 27 0.204 0.409 0.204 -1.2260 2.3805
> -0.4377
> Cluster Ag 28 0.409 0.613 0.204 0.3871 -0.0963
> -0.0275
> Cluster Ag 29 -0.409 -0.204 0.204 0.3262
> -0.1153 -0.1338
> Cluster Ag 30 -0.204 0.000 0.204 0.9592 -0.5738
> -0.0823
> Cluster Ag 31 0.204 0.204 0.409 0.5413 0.4476
> -0.0550
> Cluster Ag 32 0.409 0.409 0.409 -0.3161 -0.2168
> -0.1527
> Cluster Ag 33 0.613 0.613 0.409 -0.6814 0.5993
> -0.2307
> Cluster Ag 34 -0.204 -0.204 0.409 0.2552 0.4818
> -0.0729
> Cluster Ag 35 0.000 0.000 0.409 0.0408 0.0414
> -0.0155
> Cluster Ag 36 0.409 0.204 0.613 -0.8836 -0.7443
> 0.2603
> Cluster Ag 37 0.613 0.409 0.613 -0.2645 -0.3151
> -0.2842
> Cluster Ag 38 0.817 0.613 0.613 -0.2692 -0.2904
> -0.2710
> Cluster Ag 39 0.000 -0.204 0.613 0.7939 -0.8404
> 0.2681
> Cluster Ag 40 0.204 0.000 0.613 -0.9573 -0.0950
> -0.1476
> Cluster Ag 41 -0.409 0.204 -0.204 -0.0251
> 0.1413 0.8754
> Cluster Ag 42 -0.204 0.409 -0.204 0.2609 2.5060
> -0.0260
> Cluster Ag 43 0.000 0.613 -0.204 0.0891 -0.0179
> -0.5820
> Cluster Ag 44 -0.817 -0.204 -0.204 0.0411
> -0.1423 -0.0371
> Cluster Ag 45 -0.613 0.000 -0.204 2.3046
> -0.1273 -0.3149
> Cluster Ag 46 -0.204 0.204 0.000 0.1441 0.1891
> 0.4334
> Cluster Ag 47 0.000 0.409 0.000 0.1110 -0.0916
> -0.3021
> Cluster Ag 48 0.204 0.613 0.000 1.7741 0.8838
> -0.5496
> Cluster Ag 49 -0.613 -0.204 0.000 -0.5728
> 0.6002 0.5888
> Cluster Ag 50 -0.409 0.000 0.000 -0.3661 0.1889
> -0.3877
> Cluster Ag 51 0.000 0.409 0.409 -0.9799 -0.9920
> -0.7041
> Cluster Ag 52 0.204 0.613 0.409 0.5592 0.5398
> 0.2283
> Cluster Ag 53 0.409 0.817 0.409 0.2324 0.0219
> 0.8539
> Cluster Ag 54 -0.409 0.000 0.409 -1.4993 2.1205
> -0.7097
> Cluster Ag 55 -0.204 0.204 0.409 -0.3122 0.1147
> 0.0698
> Cluster Ag 56 0.204 0.409 0.613 -0.0068 0.7304
> -0.0835
> Cluster Ag 57 0.409 0.613 0.613 1.3374 -0.3369
> -0.8824
> Cluster Ag 58 0.613 0.817 0.613 0.1708 0.0097
> 0.3006
> Cluster Ag 59 -0.204 0.000 0.613 0.2412 -0.0100
> 0.3912
> Cluster Ag 60 0.000 0.204 0.613 -0.2191 -0.1492
> 0.6027
> Cluster Ag 61 0.409 0.409 0.817 0.1502 -0.1929
> 0.0553
> Cluster Ag 62 0.613 0.613 0.817 0.0980 -0.2419
> 0.0734
> Cluster Ag 63 0.817 0.817 0.817 0.5492 -0.3666
> -1.9324
> Cluster Ag 64 0.000 0.000 0.817 -0.1240 -0.0202
> -0.4686
> Cluster Ag 65 0.204 0.204 0.817 -0.7004 -0.5690
> 0.2006
> Cluster Ag 66 -0.409 0.409 0.000 -1.5054
> -0.7691 -2.3209
> Cluster Ag 67 -0.204 0.613 0.000 -0.2158 0.3046
> 0.1285
> Cluster Ag 68 0.000 0.817 0.000 -0.2796 -0.1991
> -0.1788
> Cluster Ag 69 -0.817 0.000 0.000 -0.9589
> -0.5213 1.1579
> Cluster Ag 70 -0.613 0.204 0.000 0.2821 -0.1943
> -0.2747
> Cluster Ag 71 -0.204 0.409 0.204 0.2847 -0.0926
> -0.0396
> Cluster Ag 72 0.000 0.613 0.204 0.9786 -0.8756
> 0.0956
> Cluster Ag 73 0.204 0.817 0.204 -0.4605 -0.0901
> -0.1077
> Cluster Ag 74 -0.613 0.000 0.204 -0.1979
> -0.4105 -0.0193
> Cluster Ag 75 -0.409 0.204 0.204 -0.7589
> -1.6968 1.2298
> Cluster Ag 76 0.000 -0.409 -0.409 0.2119 0.8203
> -0.0629
> Cluster Ag 77 0.204 -0.204 -0.409 -0.3306
> -1.1357 -0.0166
> Cluster Ag 78 0.409 0.000 -0.409 0.3747 0.7404
> -1.7866
> Cluster Ag 79 -0.409 -0.817 -0.409 0.6604
> -0.3262 -0.4982
> Cluster Ag 80 -0.204 -0.613 -0.409 0.0260
> 0.2726 0.5296
> Cluster Ag 81 0.204 -0.409 -0.204 -1.1697
> 0.0510 -1.4964
> Cluster Ag 82 0.409 -0.204 -0.204 -0.2341
> -0.0474 0.0546
> Cluster Ag 83 0.613 0.000 -0.204 -0.4170
> -0.1297 -0.0042
> Cluster Ag 84 -0.204 -0.817 -0.204 -0.4506
> 0.5506 0.4995
> Cluster Ag 85 0.000 -0.613 -0.204 -0.0199
> 0.2624 -0.4591
> Cluster Ag 86 0.409 -0.409 0.000 -0.5095
> -0.1720 -0.2808
> Cluster Ag 87 0.613 -0.204 0.000 -1.4552
> -0.2619 -0.0281
> Cluster Ag 88 0.817 0.000 0.000 0.1955 -0.6831
> 0.5407
> Cluster Ag 89 0.000 -0.817 0.000 0.3588 0.3660
> -0.0230
> Cluster Ag 90 0.204 -0.613 0.000 -0.1350 0.4515
> -1.3540
> Cluster Ag 91 -0.409 -0.409 -0.817 -0.1335
> -0.5718 0.5483
> Cluster Ag 92 -0.204 -0.204 -0.817 -0.3027
> 0.1857 0.5561
> Cluster Ag 93 0.000 0.000 -0.817 -1.4709
> -0.4135 0.4452
> Cluster Ag 94 -0.817 -0.817 -0.817 -0.0143
> 0.0735 -0.2719
> Cluster Ag 95 -0.613 -0.613 -0.817 -0.0585
> -0.3216 -0.5952
> Cluster Ag 96 -0.204 -0.409 -0.613 -1.2468
> -3.2206 0.5695
> Cluster Ag 97 0.000 -0.204 -0.613 0.4107 0.1953
> 0.4603
> Cluster Ag 98 0.204 0.000 -0.613 0.3280 -0.1838
> 0.1072
> Cluster Ag 99 -0.613 -0.817 -0.613 -0.3420
> -1.2584 1.4216
> Cluster Ag 100 -0.409 -0.613 -0.613 -0.5109
> -0.3568 -0.3184
> Cluster Ag 101 0.000 -0.204 -0.204 0.4185
> 1.0431 0.1785
> Cluster Ag 102 0.204 0.000 -0.204 -0.3009
> 2.1678 3.1545
> Cluster Ag 103 0.409 0.204 -0.204 0.3822
> -0.5026 0.1695
> Cluster Ag 104 -0.409 -0.613 -0.204 0.1886
> 0.0421 0.0337
> Cluster Ag 105 -0.204 -0.409 -0.204 0.6404
> 0.5121 2.6134
> Cluster Ag 106 0.204 -0.204 0.000 -0.5949
> -0.5280 -0.5255
> Cluster Ag 107 0.409 0.000 0.000 -0.3757
> -0.0529 -0.0024
> Cluster Ag 108 0.613 0.204 0.000 -1.0720
> -0.0008 -0.1236
> Cluster Ag 109 -0.204 -0.613 0.000 -0.5689
> -0.0252 -0.0757
> Cluster Ag 110 0.000 -0.409 0.000 -0.3944
> 0.6959 -0.0330
> Cluster Ag 111 0.409 -0.204 0.204 -1.5810
> 1.9547 1.0041
> Cluster Ag 112 0.613 0.000 0.204 0.1659 0.5399
> 0.6711
> Cluster Ag 113 0.817 0.204 0.204 -0.4301 0.6907
> -0.0736
> Cluster Ag 114 0.000 -0.613 0.204 -0.0391
> -2.3133 0.1403
> Cluster Ag 115 0.204 -0.409 0.204 -0.2787
> -0.2522 -0.1074
> Cluster Ag 116 -0.409 -0.204 -0.613 -0.2086
> -0.4636 0.2368
> Cluster Ag 117 -0.204 0.000 -0.613 -0.3764
> -0.8997 0.4974
> Cluster Ag 118 0.000 0.204 -0.613 0.1786 0.2621
> -0.3673
> Cluster Ag 119 -0.817 -0.613 -0.613 0.5404
> 0.3315 -0.3523
> Cluster Ag 120 -0.613 -0.409 -0.613 0.9744
> 0.4829 0.2210
> Cluster Ag 121 -0.204 -0.204 -0.409 -0.3398
> 0.0290 0.1140
> Cluster Ag 122 0.000 0.000 -0.409 -0.1941
> 0.2379 -1.1315
> Cluster Ag 123 0.204 0.204 -0.409 -1.0682
> -0.6024 -1.3417
> Cluster Ag 124 -0.613 -0.613 -0.409 -0.3698
> 0.0429 0.2879
> Cluster Ag 125 -0.409 -0.409 -0.409 -0.3682
> 0.2570 0.5603
> 2.00000 2.00000 2.00000
>
>
> *topol.top:*
>
> #include "amber03.ff/forcefield.itp"
> #include "silver.itp"
>
> [ moleculetype ]
> Cluster 3
>
> [ atoms ]
> ; nr type resnr residu atom cgnr charge
> 1 Ag 1 Cluster Ag 1 0.000
> 2 Ag 1 Cluster Ag 2 0.000
> 3 Ag 1 Cluster Ag 3 0.000
> 4 Ag 1 Cluster Ag 4 0.000
> 5 Ag 1 Cluster Ag 5 0.000
> 6 Ag 1 Cluster Ag 6 0.000
> 7 Ag 1 Cluster Ag 7 0.000
> 8 Ag 1 Cluster Ag 8 0.000
> 9 Ag 1 Cluster Ag 9 0.000
> 10 Ag 1 Cluster Ag 10 0.000
> 11 Ag 1 Cluster Ag 11 0.000
> 12 Ag 1 Cluster Ag 12 0.000
> 13 Ag 1 Cluster Ag 13 0.000
> 14 Ag 1 Cluster Ag 14 0.000
> 15 Ag 1 Cluster Ag 15 0.000
> 16 Ag 1 Cluster Ag 16 0.000
> 17 Ag 1 Cluster Ag 17 0.000
> 18 Ag 1 Cluster Ag 18 0.000
> 19 Ag 1 Cluster Ag 19 0.000
> 20 Ag 1 Cluster Ag 20 0.000
> 21 Ag 1 Cluster Ag 21 0.000
> 22 Ag 1 Cluster Ag 22 0.000
> 23 Ag 1 Cluster Ag 23 0.000
> 24 Ag 1 Cluster Ag 24 0.000
> 25 Ag 1 Cluster Ag 25 0.000
> 26 Ag 1 Cluster Ag 26 0.000
> 27 Ag 1 Cluster Ag 27 0.000
> 28 Ag 1 Cluster Ag 28 0.000
> 29 Ag 1 Cluster Ag 29 0.000
> 30 Ag 1 Cluster Ag 30 0.000
> 31 Ag 1 Cluster Ag 31 0.000
> 32 Ag 1 Cluster Ag 32 0.000
> 33 Ag 1 Cluster Ag 33 0.000
> 34 Ag 1 Cluster Ag 34 0.000
> 35 Ag 1 Cluster Ag 35 0.000
> 36 Ag 1 Cluster Ag 36 0.000
> 37 Ag 1 Cluster Ag 37 0.000
> 38 Ag 1 Cluster Ag 38 0.000
> 39 Ag 1 Cluster Ag 39 0.000
> 40 Ag 1 Cluster Ag 40 0.000
> 41 Ag 1 Cluster Ag 41 0.000
> 42 Ag 1 Cluster Ag 42 0.000
> 43 Ag 1 Cluster Ag 43 0.000
> 44 Ag 1 Cluster Ag 44 0.000
> 45 Ag 1 Cluster Ag 45 0.000
> 46 Ag 1 Cluster Ag 46 0.000
> 47 Ag 1 Cluster Ag 47 0.000
> 48 Ag 1 Cluster Ag 48 0.000
> 49 Ag 1 Cluster Ag 49 0.000
> 50 Ag 1 Cluster Ag 50 0.000
> 51 Ag 1 Cluster Ag 51 0.000
> 52 Ag 1 Cluster Ag 52 0.000
> 53 Ag 1 Cluster Ag 53 0.000
> 54 Ag 1 Cluster Ag 54 0.000
> 55 Ag 1 Cluster Ag 55 0.000
> 56 Ag 1 Cluster Ag 56 0.000
> 57 Ag 1 Cluster Ag 57 0.000
> 58 Ag 1 Cluster Ag 58 0.000
> 59 Ag 1 Cluster Ag 59 0.000
> 60 Ag 1 Cluster Ag 60 0.000
> 61 Ag 1 Cluster Ag 61 0.000
> 62 Ag 1 Cluster Ag 62 0.000
> 63 Ag 1 Cluster Ag 63 0.000
> 64 Ag 1 Cluster Ag 64 0.000
> 65 Ag 1 Cluster Ag 65 0.000
> 66 Ag 1 Cluster Ag 66 0.000
> 67 Ag 1 Cluster Ag 67 0.000
> 68 Ag 1 Cluster Ag 68 0.000
> 69 Ag 1 Cluster Ag 69 0.000
> 70 Ag 1 Cluster Ag 70 0.000
> 71 Ag 1 Cluster Ag 71 0.000
> 72 Ag 1 Cluster Ag 72 0.000
> 73 Ag 1 Cluster Ag 73 0.000
> 74 Ag 1 Cluster Ag 74 0.000
> 75 Ag 1 Cluster Ag 75 0.000
> 76 Ag 1 Cluster Ag 76 0.000
> 77 Ag 1 Cluster Ag 77 0.000
> 78 Ag 1 Cluster Ag 78 0.000
> 79 Ag 1 Cluster Ag 79 0.000
> 80 Ag 1 Cluster Ag 80 0.000
> 81 Ag 1 Cluster Ag 81 0.000
> 82 Ag 1 Cluster Ag 82 0.000
> 83 Ag 1 Cluster Ag 83 0.000
> 84 Ag 1 Cluster Ag 84 0.000
> 85 Ag 1 Cluster Ag 85 0.000
> 86 Ag 1 Cluster Ag 86 0.000
> 87 Ag 1 Cluster Ag 87 0.000
> 88 Ag 1 Cluster Ag 88 0.000
> 89 Ag 1 Cluster Ag 89 0.000
> 90 Ag 1 Cluster Ag 90 0.000
> 91 Ag 1 Cluster Ag 91 0.000
> 92 Ag 1 Cluster Ag 92 0.000
> 93 Ag 1 Cluster Ag 93 0.000
> 94 Ag 1 Cluster Ag 94 0.000
> 95 Ag 1 Cluster Ag 95 0.000
> 96 Ag 1 Cluster Ag 96 0.000
> 97 Ag 1 Cluster Ag 97 0.000
> 98 Ag 1 Cluster Ag 98 0.000
> 99 Ag 1 Cluster Ag 99 0.000
> 100 Ag 1 Cluster Ag 100 0.000
> 101 Ag 1 Cluster Ag 101 0.000
> 102 Ag 1 Cluster Ag 102 0.000
> 103 Ag 1 Cluster Ag 103 0.000
> 104 Ag 1 Cluster Ag 104 0.000
> 105 Ag 1 Cluster Ag 105 0.000
> 106 Ag 1 Cluster Ag 106 0.000
> 107 Ag 1 Cluster Ag 107 0.000
> 108 Ag 1 Cluster Ag 108 0.000
> 109 Ag 1 Cluster Ag 109 0.000
> 110 Ag 1 Cluster Ag 110 0.000
> 111 Ag 1 Cluster Ag 111 0.000
> 112 Ag 1 Cluster Ag 112 0.000
> 113 Ag 1 Cluster Ag 113 0.000
> 114 Ag 1 Cluster Ag 114 0.000
> 115 Ag 1 Cluster Ag 115 0.000
> 116 Ag 1 Cluster Ag 116 0.000
> 117 Ag 1 Cluster Ag 117 0.000
> 118 Ag 1 Cluster Ag 118 0.000
> 119 Ag 1 Cluster Ag 119 0.000
> 120 Ag 1 Cluster Ag 120 0.000
> 121 Ag 1 Cluster Ag 121 0.000
> 122 Ag 1 Cluster Ag 122 0.000
> 123 Ag 1 Cluster Ag 123 0.000
> 124 Ag 1 Cluster Ag 124 0.000
> 125 Ag 1 Cluster Ag 125 0.000
>
> [ bonds ]
> 1 2 5
>
> [ system ]
> Bulk silver
>
> [ molecules ]
> Cluster 1
>
> *silver.itp:*
>
> [ atomtypes ]
> ; type mass charge ptype c6 c12
> Ag 107.8682 0.0 A 2.6169e-3 2.5231e-6
>
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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