Hi Albert,
Yes, that is the correct format for POPE. The TER cards signalize the end of a lipid molecule,
which each consists of three different residues, as in your case with a palmitoyl chain (PA),
a phosphatidylethanolamine moiety (PE) and an oleoyl chain (OL). Had there been TER cards
between each residue, the phospholipids would have been split into its component tails and head
group.
Best regards,
Åge
> Date: Wed, 23 May 2012 09:23:59 +0200
> From: mailmd2011.gmail.com
> To: amber.ambermd.org
> Subject: Re: [AMBER] was the bug fixed for tleap?
>
> 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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> >> http://lists.ambermd.org/mailman/listinfo/amber
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> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
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Received on Wed May 23 2012 - 05:00:03 PDT
