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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
==================================================
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