[gmx-users] grompp Warning: atom name 20 in p2.top and p2.pdb does not match
Justin Lemkul
jalemkul at vt.edu
Mon Sep 23 03:22:54 CEST 2013
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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