[gmx-users] grompp Warning: atom name 20 in p2.top and p2.pdb does not match
Nilesh Dhumal
ndhumal at andrew.cmu.edu
Mon Sep 23 03:32:23 CEST 2013
Thanks.
I have total 128 EMI and 128 ETS. To find the solution I test for 2 EMI
and 2 ETS.
How can I define for 128 EMI and 128 ETS ?
Nilesh
>
> On 9/22/13 9:18 PM, Nilesh Dhumal wrote:
>> Sorry to paste big files here. (.pdb file and processed.top )
>>
>>
>> pdb file.
>>
>> TITLE Protein
>> REMARK THIS IS A SIMULATION BOX
>> CRYST1 34.775 34.775 34.775 90.00 90.00 90.00 P 1 1
>> MODEL 1
>> ATOM 1 C EMI 1 4.659 30.489 15.747 1.00 0.00
>> ATOM 2 C2 EMI 1 5.238 30.284 14.495 1.00 0.00
>> ATOM 3 N3 EMI 1 6.415 30.946 14.495 1.00 0.00
>> ATOM 4 C4 EMI 1 6.627 31.499 15.682 1.00 0.00
>> ATOM 5 N5 EMI 1 5.595 31.153 16.470 1.00 0.00
>> ATOM 6 C6 EMI 1 5.462 31.463 17.884 1.00 0.00
>> ATOM 7 C7 EMI 1 4.501 30.509 18.615 1.00 0.00
>> ATOM 8 C8 EMI 1 7.321 30.993 13.363 1.00 0.00
>> ATOM 9 H9 EMI 1 3.672 30.193 16.130 1.00 0.00
>> ATOM 10 H10 EMI 1 4.839 29.853 13.640 1.00 0.00
>> ATOM 11 H11 EMI 1 7.514 32.004 16.038 1.00 0.00
>> ATOM 12 H12 EMI 1 7.951 31.796 13.329 1.00 0.00
>> ATOM 13 H13 EMI 1 7.967 30.145 13.270 1.00 0.00
>> ATOM 14 H14 EMI 1 6.890 31.170 12.362 1.00 0.00
>> ATOM 15 H15 EMI 1 5.214 32.491 18.125 1.00 0.00
>> ATOM 16 H16 EMI 1 6.495 31.335 18.302 1.00 0.00
>> ATOM 17 H17 EMI 1 4.834 29.492 18.590 1.00 0.00
>> ATOM 18 H18 EMI 1 4.337 30.767 19.685 1.00 0.00
>> ATOM 19 H19 EMI 1 3.486 30.669 18.338 1.00 0.00
>> ATOM 20 S20 ETS 2 13.817 2.976 33.669 1.00 0.00
>> ATOM 21 O21 ETS 2 15.031 2.685 34.347 1.00 0.00
>> ATOM 22 O22 ETS 2 14.005 3.313 32.237 1.00 0.00
>> ATOM 23 O23 ETS 2 12.775 1.970 33.860 1.00 0.00
>> ATOM 24 O24 ETS 2 13.303 4.314 34.278 1.00 0.00
>> ATOM 25 C25 ETS 2 12.361 5.280 33.781 1.00 0.00
>> ATOM 26 C26 ETS 2 12.277 6.501 34.666 1.00 0.00
>> ATOM 27 H27 ETS 2 12.582 5.675 32.806 1.00 0.00
>> ATOM 28 H28 ETS 2 11.377 4.787 33.550 1.00 0.00
>> ATOM 29 H29 ETS 2 11.686 6.245 35.492 1.00 0.00
>> ATOM 30 H30 ETS 2 13.256 6.810 34.975 1.00 0.00
>> ATOM 31 H31 ETS 2 11.856 7.349 34.171 1.00 0.00
>> ATOM 32 C EMI 3 25.075 29.706 5.816 1.00 0.00
>> ATOM 33 C2 EMI 3 24.256 29.876 6.894 1.00 0.00
>> ATOM 34 N3 EMI 3 25.074 30.288 7.940 1.00 0.00
>> ATOM 35 C4 EMI 3 26.335 30.336 7.464 1.00 0.00
>> ATOM 36 N5 EMI 3 26.369 29.867 6.216 1.00 0.00
>> ATOM 37 C6 EMI 3 27.586 29.761 5.460 1.00 0.00
>> ATOM 38 C7 EMI 3 27.397 29.088 4.106 1.00 0.00
>> ATOM 39 C8 EMI 3 24.601 30.404 9.351 1.00 0.00
>> ATOM 40 H9 EMI 3 24.815 29.446 4.790 1.00 0.00
>> ATOM 41 H10 EMI 3 23.203 29.817 6.920 1.00 0.00
>> ATOM 42 H11 EMI 3 27.238 30.558 8.074 1.00 0.00
>> ATOM 43 H12 EMI 3 24.321 29.435 9.759 1.00 0.00
>> ATOM 44 H13 EMI 3 25.411 30.876 9.880 1.00 0.00
>> ATOM 45 H14 EMI 3 23.735 31.092 9.515 1.00 0.00
>> ATOM 46 H15 EMI 3 28.216 29.130 6.169 1.00 0.00
>> ATOM 47 H16 EMI 3 28.027 30.763 5.434 1.00 0.00
>> ATOM 48 H17 EMI 3 26.886 29.695 3.344 1.00 0.00
>> ATOM 49 H18 EMI 3 28.366 28.886 3.715 1.00 0.00
>> ATOM 50 H19 EMI 3 26.842 28.200 3.880 1.00 0.00
>> ATOM 51 S20 ETS 4 26.876 17.203 7.791 1.00 0.00
>> ATOM 52 O21 ETS 4 28.030 16.750 7.061 1.00 0.00
>> ATOM 53 O22 ETS 4 25.656 16.428 7.528 1.00 0.00
>> ATOM 54 O23 ETS 4 27.112 17.470 9.202 1.00 0.00
>> ATOM 55 O24 ETS 4 26.578 18.733 7.129 1.00 0.00
>> ATOM 56 C25 ETS 4 26.215 18.995 5.843 1.00 0.00
>> ATOM 57 C26 ETS 4 27.436 19.133 4.921 1.00 0.00
>> ATOM 58 H27 ETS 4 25.607 18.170 5.486 1.00 0.00
>> ATOM 59 H28 ETS 4 25.530 19.872 5.774 1.00 0.00
>> ATOM 60 H29 ETS 4 28.107 19.910 5.179 1.00 0.00
>> ATOM 61 H30 ETS 4 27.944 18.247 4.832 1.00 0.00
>> ATOM 62 H31 ETS 4 27.138 19.330 3.927 1.00 0.00
>> TER
>> ENDMDL
>
> <snip>
>
>> [ molecules ]
>> ; Compound #mols
>> EMI 2
>> ETS 2
>>
>
> As I suspected, your molecules are simply out of order. Your topology
> specifies
> EMI-EMI-ETS-ETS, but the coordinate file lists the molecules as
> EMI-ETS-EMI-ETS,
> hence the mismatch. The "Protein" [moleculetype] seems superfluous, but
> would
> be the appropriate solution for this case since it specifies
> EMI-ETS-EMI-ETS all
> in one [moleculetype] definition.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>
> ==================================================
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