Hello Ben:
thanks for kind comments. I convert the md output pdb with command
ambpdb and here is one of the lipid I get:
ATOM 1 C116 PA 1 11.254 11.537 -5.901 1.00
0.00 C
ATOM 2 H16R PA 1 11.155 12.131 -6.812 1.00
0.00 H
ATOM 3 H16S PA 1 10.242 11.196 -5.671 1.00
0.00 H
ATOM 4 H16T PA 1 11.872 10.663 -6.118 1.00
0.00 H
ATOM 5 C115 PA 1 11.714 12.284 -4.580 1.00
0.00 C
ATOM 6 H15R PA 1 12.709 12.722 -4.688 1.00
0.00 H
ATOM 7 H15S PA 1 11.066 13.116 -4.296 1.00
0.00 H
ATOM 8 C114 PA 1 11.608 11.376 -3.347 1.00
0.00 C
ATOM 9 H14R PA 1 10.595 10.989 -3.213 1.00
0.00 H
ATOM 10 H14S PA 1 12.126 10.443 -3.581 1.00
0.00 H
ATOM 11 C113 PA 1 11.978 12.037 -2.086 1.00
0.00 C
ATOM 12 H13R PA 1 11.163 12.654 -1.701 1.00
0.00 H
ATOM 13 H13S PA 1 12.828 12.715 -2.184 1.00
0.00 H
ATOM 14 C112 PA 1 12.329 11.064 -0.923 1.00
0.00 C
ATOM 15 H12R PA 1 11.431 10.492 -0.682 1.00
0.00 H
ATOM 16 H12S PA 1 13.078 10.293 -1.113 1.00
0.00 H
ATOM 17 C111 PA 1 12.718 11.847 0.364 1.00
0.00 C
ATOM 18 H11R PA 1 13.495 12.591 0.174 1.00
0.00 H
ATOM 19 H11S PA 1 11.820 12.444 0.536 1.00
0.00 H
ATOM 20 C110 PA 1 13.036 10.884 1.492 1.00
0.00 C
ATOM 21 H10R PA 1 12.182 10.322 1.876 1.00
0.00 H
ATOM 22 H10S PA 1 13.794 10.178 1.146 1.00
0.00 H
ATOM 23 C19 PA 1 13.795 11.598 2.627 1.00
0.00 C
ATOM 24 H9R PA 1 14.855 11.643 2.367 1.00
0.00 H
ATOM 25 H9S PA 1 13.484 12.643 2.695 1.00
0.00 H
ATOM 26 C18 PA 1 13.635 10.931 4.000 1.00
0.00 C
ATOM 27 H8R PA 1 12.582 10.827 4.269 1.00
0.00 H
ATOM 28 H8S PA 1 13.806 9.857 3.905 1.00
0.00 H
ATOM 29 C17 PA 1 14.430 11.464 5.146 1.00
0.00 C
ATOM 30 H7R PA 1 15.473 11.186 4.979 1.00
0.00 H
ATOM 31 H7S PA 1 14.409 12.553 5.220 1.00
0.00 H
ATOM 32 C16 PA 1 13.971 10.738 6.468 1.00
0.00 C
ATOM 33 H6R PA 1 12.893 10.746 6.639 1.00
0.00 H
ATOM 34 H6S PA 1 14.142 9.679 6.266 1.00
0.00 H
ATOM 35 C15 PA 1 14.894 11.109 7.688 1.00
0.00 C
ATOM 36 H5R PA 1 15.958 11.050 7.450 1.00
0.00 H
ATOM 37 H5S PA 1 14.624 12.111 8.028 1.00
0.00 H
ATOM 38 C14 PA 1 14.613 10.101 8.866 1.00
0.00 C
ATOM 39 H4R PA 1 13.551 10.180 9.108 1.00
0.00 H
ATOM 40 H4S PA 1 14.784 9.120 8.419 1.00
0.00 H
ATOM 41 C13 PA 1 15.538 10.499 10.028 1.00
0.00 C
ATOM 42 H3R PA 1 16.563 10.518 9.650 1.00
0.00 H
ATOM 43 H3S PA 1 15.315 11.505 10.389 1.00
0.00 H
ATOM 44 C12 PA 1 15.447 9.471 11.155 1.00
0.00 C
ATOM 45 H2R PA 1 14.474 9.436 11.651 1.00
0.00 H
ATOM 46 H2S PA 1 15.819 8.505 10.806 1.00
0.00 H
ATOM 47 C11 PE 2 16.369 9.990 12.217 1.00
0.00 C
ATOM 48 O12 PE 2 15.967 10.593 13.252 1.00
0.00 O
ATOM 49 O11 PE 2 17.638 9.799 11.841 1.00
0.00 O
ATOM 50 C1 PE 2 18.798 10.548 12.516 1.00
0.00 C
ATOM 51 HR PE 2 18.662 11.620 12.683 1.00
0.00 H
ATOM 52 HS PE 2 19.045 10.113 13.488 1.00
0.00 H
ATOM 53 C2 PE 2 19.951 10.455 11.490 1.00
0.00 C
ATOM 54 HX PE 2 20.068 9.459 11.057 1.00
0.00 H
ATOM 55 C3 PE 2 21.335 10.875 12.130 1.00
0.00 C
ATOM 56 HA PE 2 21.798 9.981 12.555 1.00
0.00 H
ATOM 57 HB PE 2 21.897 11.377 11.338 1.00
0.00 H
ATOM 58 O31 PE 2 21.184 11.864 13.131 1.00
0.00 O
ATOM 59 P31 PE 2 21.938 11.790 14.569 1.00
0.00 P
ATOM 60 O32 PE 2 20.955 12.709 15.438 1.00
0.00 O
ATOM 61 C31 PE 2 20.054 12.053 16.362 1.00
0.00 C
ATOM 62 H1A PE 2 19.478 11.280 15.847 1.00
0.00 H
ATOM 63 H1B PE 2 20.531 11.440 17.131 1.00
0.00 H
ATOM 64 C32 PE 2 19.243 13.164 16.982 1.00
0.00 C
ATOM 65 H2A PE 2 18.530 12.811 17.728 1.00
0.00 H
ATOM 66 H2B PE 2 19.958 13.875 17.397 1.00
0.00 H
ATOM 67 N31 PE 2 18.445 13.883 15.895 1.00
0.00 N
ATOM 68 HN1A PE 2 19.074 14.054 15.094 1.00
0.00 H
ATOM 69 HN1B PE 2 17.748 13.288 15.417 1.00
0.00 H
ATOM 70 HN1C PE 2 18.036 14.797 16.149 1.00
0.00 H
ATOM 71 O33 PE 2 23.301 12.354 14.650 1.00
0.00 O
ATOM 72 O34 PE 2 21.994 10.353 14.965 1.00
0.00 O
ATOM 73 O21 PE 2 19.708 11.378 10.404 1.00
0.00 O
ATOM 74 C21 PE 2 20.288 11.219 9.235 1.00
0.00 C
ATOM 75 O22 PE 2 21.187 10.466 9.041 1.00
0.00 O
ATOM 76 C12 OL 3 19.670 11.952 8.119 1.00
0.00 C
ATOM 77 H2R OL 3 20.144 12.936 8.107 1.00
0.00 H
ATOM 78 H2S OL 3 18.649 12.210 8.409 1.00
0.00 H
ATOM 79 C13 OL 3 19.743 11.328 6.715 1.00
0.00 C
ATOM 80 H3R OL 3 19.207 10.385 6.842 1.00
0.00 H
ATOM 81 H3S OL 3 20.757 11.091 6.388 1.00
0.00 H
ATOM 82 C14 OL 3 19.069 12.255 5.594 1.00
0.00 C
ATOM 83 H4R OL 3 19.548 13.236 5.630 1.00
0.00 H
ATOM 84 H4S OL 3 18.069 12.485 5.969 1.00
0.00 H
ATOM 85 C15 OL 3 19.126 11.618 4.183 1.00
0.00 C
ATOM 86 H5R OL 3 18.644 10.662 4.398 1.00
0.00 H
ATOM 87 H5S OL 3 20.181 11.564 3.905 1.00
0.00 H
ATOM 88 C16 OL 3 18.317 12.430 3.143 1.00
0.00 C
ATOM 89 H6R OL 3 18.406 13.507 3.300 1.00
0.00 H
ATOM 90 H6S OL 3 17.252 12.201 3.212 1.00
0.00 H
ATOM 91 C17 OL 3 18.777 12.212 1.683 1.00
0.00 C
ATOM 92 H7R OL 3 18.904 11.168 1.390 1.00
0.00 H
ATOM 93 H7S OL 3 19.779 12.640 1.611 1.00
0.00 H
ATOM 94 C18 OL 3 17.819 13.010 0.733 1.00
0.00 C
ATOM 95 H8R OL 3 17.387 13.897 1.201 1.00
0.00 H
ATOM 96 H8S OL 3 16.925 12.478 0.400 1.00
0.00 H
ATOM 97 C19 OL 3 18.510 13.500 -0.571 1.00
0.00 C
ATOM 98 H9R OL 3 18.334 12.838 -1.415 1.00
0.00 H
ATOM 99 C110 OL 3 19.119 14.712 -0.700 1.00
0.00 C
ATOM 100 H10R OL 3 19.471 14.975 -1.694 1.00
0.00 H
ATOM 101 C111 OL 3 19.524 15.599 0.430 1.00
0.00 C
ATOM 102 H11R OL 3 20.517 16.047 0.350 1.00
0.00 H
ATOM 103 H11S OL 3 19.434 14.999 1.338 1.00
0.00 H
ATOM 104 C112 OL 3 18.699 16.825 0.693 1.00
0.00 C
ATOM 105 H12R OL 3 17.645 16.592 0.859 1.00
0.00 H
ATOM 106 H12S OL 3 18.694 17.387 -0.243 1.00
0.00 H
ATOM 107 C113 OL 3 19.170 17.533 2.012 1.00
0.00 C
ATOM 108 H13R OL 3 18.491 18.373 2.176 1.00
0.00 H
ATOM 109 H13S OL 3 20.144 17.976 1.791 1.00
0.00 H
ATOM 110 C114 OL 3 19.207 16.654 3.271 1.00
0.00 C
ATOM 111 H14R OL 3 20.163 16.132 3.194 1.00
0.00 H
ATOM 112 H14S OL 3 18.395 15.927 3.332 1.00
0.00 H
ATOM 113 C115 OL 3 19.298 17.250 4.710 1.00
0.00 C
ATOM 114 H15R OL 3 18.321 17.719 4.846 1.00
0.00 H
ATOM 115 H15S OL 3 20.122 17.951 4.563 1.00
0.00 H
ATOM 116 C116 OL 3 19.521 16.169 5.759 1.00
0.00 C
ATOM 117 H16R OL 3 20.427 15.572 5.636 1.00
0.00 H
ATOM 118 H16S OL 3 18.720 15.429 5.697 1.00
0.00 H
ATOM 119 C117 OL 3 19.418 16.820 7.208 1.00
0.00 C
ATOM 120 H17R OL 3 18.436 17.270 7.369 1.00
0.00 H
ATOM 121 H17S OL 3 20.231 17.543 7.303 1.00
0.00 H
ATOM 122 C118 OL 3 19.641 15.812 8.389 1.00
0.00 C
ATOM 123 H18R OL 3 20.489 15.132 8.283 1.00
0.00 H
ATOM 124 H18S OL 3 18.828 15.085 8.329 1.00
0.00 H
ATOM 125 H18T OL 3 19.775 16.372 9.316 1.00
0.00 H
TER
As we can see, there is no more additional 'TER' in the lipids, but the
lipids was still divided into three moiety..... I am just wondering is
it the correct format?
thank you very much
best
Albert
On 05/19/2012 02:03 AM, Benjamin D Madej wrote:
> Hi Albert,
>
> We've filed a bug report for leap and as soon as someone can take a good look at it, they will.
>
> The official workaround for this problem is to save a prmtop and mdcrd file from LEaP (saveAmberParam) then use ambpdb to save a pdb file (see the manual). ambpdb correctly formats the pdb files for lipid11. This is what we've been doing for a correct pdb.
>
> Thanks,
> Ben
>
> On May 18, 2012, at 11:43, "Albert"<mailmd2011.gmail.com> wrote:
>
>> hello:
>>
>> Many users found that there is a bug in Amber 12's tleap: there are
>> incorrect TER for saving lipids PDB.....I am wondering, is there any
>> bugfix ready for this problem?
>>
>> thx
>>
>> Albert
>> _______________________________________________
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Received on Wed May 23 2012 - 00:30:03 PDT
