Dear All,
I would like to simulate a micelle(n-Dodecyl-¦Â-D-maltopyranoside, DDM)in the water with Amber16. Last time I have sent similar question and got some help from Qinghua Liao and Abel Stephane, thanks for their kindly advice.
I firstly used antechamber to generate the mol2 file with a single DDM molecule, then parmchk to .frcmod file, then leap to .lib file(I sourced leaprc.ff99SB and leaprc.gaff2 or leaprc.GLYCAM_06j-1--both I have tried), everyrhing went well. Then I used leap(I also sourced leaprc.ff99SB and leaprc.gaff2 or leaprc.GLYCAM_06j-1) again to generate the prmtop file and get "FATAL: Atom **** does not have a type", all atoms of my DDM_130.pdb not in the templates. And I have tried several force fields such as leaprc.ff14SB, but also the same error. My idea is that either due to the source problem, maybe I need to source other proper force fields, but I don't know which should I use or the format of my 130 units DDM micelle pdb file is not in the proper way. Here I list one DDM molecule, and I wish someone could help me with my problem.
ATOM 1 C1 AMT 1 5.803 8.114 31.343 1.00 0.00
ATOM 2 H1 AMT 1 6.802 7.690 31.267 1.00 0.00
ATOM 3 O1 AMT 1 4.952 7.485 30.457 1.00 0.00
ATOM 4 C2 AMT 1 5.261 7.940 32.761 1.00 0.00
ATOM 5 H2 AMT 1 5.994 8.397 33.429 1.00 0.00
ATOM 6 O2 AMT 1 5.060 6.601 33.090 1.00 0.00
ATOM 7 HO2 AMT 1 4.570 6.531 33.892 1.00 0.00
ATOM 8 C3 AMT 1 3.938 8.685 32.914 1.00 0.00
ATOM 9 H3 AMT 1 3.210 8.191 32.280 1.00 0.00
ATOM 10 O3 AMT 1 3.424 8.600 34.208 1.00 0.00
ATOM 11 HO3 AMT 1 3.284 9.464 34.561 1.00 0.00
ATOM 12 C4 AMT 1 4.108 10.139 32.471 1.00 0.00
ATOM 13 H4 AMT 1 4.746 10.661 33.174 1.00 0.00
ATOM 14 O4 AMT 1 2.892 10.833 32.476 1.00 0.00
ATOM 15 HO4 AMT 1 3.051 11.764 32.475 1.00 0.00
ATOM 16 C5 AMT 1 4.779 10.236 31.096 1.00 0.00
ATOM 17 H5 AMT 1 4.083 9.873 30.340 1.00 0.00
ATOM 18 O5 AMT 1 5.959 9.464 31.055 1.00 0.00
ATOM 19 C6 AMT 1 5.153 11.659 30.728 1.00 0.00
ATOM 20 H61 AMT 1 4.239 12.240 30.644 1.00 0.00
ATOM 21 H62 AMT 1 5.644 11.642 29.758 1.00 0.00
ATOM 22 O6 AMT 1 6.000 12.188 31.708 1.00 0.00
ATOM 23 HO6 AMT 1 5.974 13.129 31.678 1.00 0.00
ATOM 24 C1 BMG 2 6.303 6.313 26.645 1.00 0.00
ATOM 25 H1 BMG 2 6.187 5.262 26.945 1.00 0.00
ATOM 26 O1 BMG 2 6.692 6.390 25.338 1.00 0.00
ATOM 27 C2 BMG 2 7.342 6.979 27.502 1.00 0.00
ATOM 28 H2 BMG 2 7.460 7.986 27.116 1.00 0.00
ATOM 29 O2 BMG 2 8.588 6.371 27.380 1.00 0.00
ATOM 30 HO2 BMG 2 9.270 7.019 27.313 1.00 0.00
ATOM 31 C3 BMG 2 6.865 7.026 28.958 1.00 0.00
ATOM 32 H3 BMG 2 6.797 5.998 29.320 1.00 0.00
ATOM 33 O3 BMG 2 7.788 7.638 29.802 1.00 0.00
ATOM 34 HO3 BMG 2 7.718 8.577 29.738 1.00 0.00
ATOM 35 C4 BMG 2 5.473 7.648 29.060 1.00 0.00
ATOM 36 H4 BMG 2 5.511 8.693 28.781 1.00 0.00
ATOM 37 C5 BMG 2 4.529 6.950 28.076 1.00 0.00
ATOM 38 H5 BMG 2 4.385 5.913 28.402 1.00 0.00
ATOM 39 O5 BMG 2 5.077 6.965 26.789 1.00 0.00
ATOM 40 C6 BMG 2 3.157 7.595 28.012 1.00 0.00
ATOM 41 H61 BMG 2 2.681 7.475 28.983 1.00 0.00
ATOM 42 H62 BMG 2 2.565 7.070 27.268 1.00 0.00
ATOM 43 O6 BMG 2 3.300 8.946 27.684 1.00 0.00
ATOM 44 HO6 BMG 2 2.991 9.483 28.393 1.00 0.00
ATOM 45 C1 C12 3 5.664 5.727 24.471 1.00 0.00
ATOM 46 H11 C12 3 4.697 6.214 24.601 1.00 0.00
ATOM 47 H12 C12 3 5.544 4.683 24.762 1.00 0.00
ATOM 48 C2 C12 3 6.096 5.813 23.018 1.00 0.00
ATOM 49 H21 C12 3 7.071 5.342 22.923 1.00 0.00
ATOM 50 H22 C12 3 6.230 6.861 22.762 1.00 0.00
ATOM 51 C3 C12 3 5.098 5.159 22.061 1.00 0.00
ATOM 52 H31 C12 3 4.123 5.632 22.173 1.00 0.00
ATOM 53 H32 C12 3 4.962 4.113 22.334 1.00 0.00
ATOM 54 C4 C12 3 5.532 5.244 20.596 1.00 0.00
ATOM 55 H41 C12 3 6.507 4.772 20.483 1.00 0.00
ATOM 56 H42 C12 3 5.667 6.289 20.322 1.00 0.00
ATOM 57 C5 C12 3 4.539 4.592 19.632 1.00 0.00
ATOM 58 H51 C12 3 3.564 5.063 19.747 1.00 0.00
ATOM 59 H52 C12 3 4.405 3.547 19.907 1.00 0.00
ATOM 60 C6 C12 3 4.971 4.677 18.168 1.00 0.00
ATOM 61 H61 C12 3 5.946 4.205 18.053 1.00 0.00
ATOM 62 H62 C12 3 5.105 5.722 17.893 1.00 0.00
ATOM 63 C7 C12 3 3.978 4.025 17.205 1.00 0.00
ATOM 64 H71 C12 3 3.003 4.498 17.319 1.00 0.00
ATOM 65 H72 C12 3 3.843 2.980 17.480 1.00 0.00
ATOM 66 C8 C12 3 4.411 4.109 15.740 1.00 0.00
ATOM 67 H81 C12 3 5.386 3.637 15.626 1.00 0.00
ATOM 68 H82 C12 3 4.546 5.154 15.464 1.00 0.00
ATOM 69 C9 C12 3 3.419 3.457 14.777 1.00 0.00
ATOM 70 H91 C12 3 2.444 3.928 14.892 1.00 0.00
ATOM 71 H92 C12 3 3.286 2.412 15.053 1.00 0.00
ATOM 72 C10 C12 3 3.850 3.541 13.312 1.00 0.00
ATOM 73 H101 C12 3 4.825 3.069 13.196 1.00 0.00
ATOM 74 H102 C12 3 3.984 4.586 13.036 1.00 0.00
ATOM 75 C11 C12 3 2.858 2.890 12.348 1.00 0.00
ATOM 76 H111 C12 3 1.884 3.363 12.461 1.00 0.00
ATOM 77 H112 C12 3 2.723 1.845 12.622 1.00 0.00
ATOM 78 C12 C12 3 3.297 2.977 10.886 1.00 0.00
ATOM 79 H121 C12 3 3.394 4.010 10.564 1.00 0.00
ATOM 80 H122 C12 3 2.578 2.492 10.231 1.00 0.00
ATOM 81 H123 C12 3 4.258 2.492 10.736 1.00 0.00
Any suggestions would be greatly appreciated.
Thank you in advance!
All the best,
Meng Wu
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Received on Sat Jul 15 2017 - 01:30:03 PDT
