It seems some of your atoms do not have types assigned in whatever
residue template(s) you are using for the atoms in question.
Do you know what an atom type is? If not, I suggest reading a tutorial
in which a new residue is defined.
Every nonstandard residue you create needs a template file to map atom
names to types, and define connectivity and charges.
Bill
On 7/15/17 1:03 AM, Meng Wu wrote:
> 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 - 02:30:03 PDT
