Yep
please see
http://ambermd.org/tutorials/advanced/tutorial16/ and the manual
S
________________________________________
De : James Starlight [jmsstarlight.gmail.com]
Envoyé : mercredi 16 août 2017 19:57
À : AMBER Mailing List
Objet : Re: [AMBER] charmmlipid2amber.py with Charm-gui lipids
and does it normal that one lipid molecule is considered as tree
different residues now?
J,
2017-08-16 18:18 GMT+02:00 ABEL Stephane <Stephane.ABEL.cea.fr>:
> Hello,
>
> Yeap this normal. THis approach is used by Amber to simulate lipid systems such as membrane (see the manual for details)
>
> Stéphane
>
> ________________________________________
> De : James Starlight [jmsstarlight.gmail.com]
> Envoyé : mercredi 16 août 2017 17:54
> À : AMBER Mailing List
> Objet : [AMBER] charmmlipid2amber.py with Charm-gui lipids
>
> Hello,
>
> using charmmlipid2amber.py I converted the charm-gui lipids to the amber format.
>
> This is a charm-gui input for 1 lidip:
> HETATM 5021 N POPC 1 61.437 11.706 76.909 1.00 0.00 MEMB N
> HETATM 5022 C12 POPC 1 60.270 12.523 76.385 1.00 0.00 MEMB C
> HETATM 5023 H12A POPC 1 60.666 13.234 75.669 1.00 0.00 MEMB H
> HETATM 5024 H12B POPC 1 59.904 13.131 77.217 1.00 0.00 MEMB H
> HETATM 5025 C13 POPC 1 62.013 10.785 75.885 1.00 0.00 MEMB C
> HETATM 5026 H13A POPC 1 62.438 11.312 75.036 1.00 0.00 MEMB H
> HETATM 5027 H13B POPC 1 62.825 10.206 76.317 1.00 0.00 MEMB H
> HETATM 5028 H13C POPC 1 61.275 10.086 75.513 1.00 0.00 MEMB H
> HETATM 5029 C14 POPC 1 62.511 12.640 77.320 1.00 0.00 MEMB C
> HETATM 5030 H14A POPC 1 62.944 13.114 76.446 1.00 0.00 MEMB H
> HETATM 5031 H14B POPC 1 62.110 13.448 77.926 1.00 0.00 MEMB H
> HETATM 5032 H14C POPC 1 63.293 12.118 77.844 1.00 0.00 MEMB H
> HETATM 5033 C15 POPC 1 60.956 10.903 78.081 1.00 0.00 MEMB C
> HETATM 5034 H15A POPC 1 60.724 11.540 78.924 1.00 0.00 MEMB H
> HETATM 5035 H15B POPC 1 61.698 10.182 78.389 1.00 0.00 MEMB H
> HETATM 5036 H15C POPC 1 60.042 10.371 77.808 1.00 0.00 MEMB H
> HETATM 5037 C11 POPC 1 59.042 11.806 75.756 1.00 0.00 MEMB C
> HETATM 5038 H11A POPC 1 59.405 11.262 74.850 1.00 0.00 MEMB H
> HETATM 5039 H11B POPC 1 58.355 12.595 75.363 1.00 0.00 MEMB H
> HETATM 5040 P POPC 1 57.053 11.363 77.439 1.00 0.00 MEMB P
> HETATM 5041 O13 POPC 1 57.452 12.587 78.178 1.00 0.00 MEMB O
> HETATM 5042 O14 POPC 1 56.546 10.245 78.289 1.00 0.00 MEMB O
> HETATM 5043 O12 POPC 1 58.374 10.902 76.663 1.00 0.00 MEMB O
> HETATM 5044 O11 POPC 1 56.037 11.754 76.295 1.00 0.00 MEMB O
> HETATM 5045 C1 POPC 1 55.362 10.795 75.477 1.00 0.00 MEMB C
> HETATM 5046 HA POPC 1 54.345 11.170 75.235 1.00 0.00 MEMB H
> HETATM 5047 HB POPC 1 55.222 9.815 75.992 1.00 0.00 MEMB H
> HETATM 5048 C2 POPC 1 56.094 10.548 74.132 1.00 0.00 MEMB C
> HETATM 5049 HS POPC 1 57.145 10.281 74.404 1.00 0.00 MEMB H
> HETATM 5050 O21 POPC 1 56.015 11.762 73.320 1.00 0.00 MEMB O
> HETATM 5051 C21 POPC 1 57.036 11.881 72.487 1.00 0.00 MEMB C
> HETATM 5052 O22 POPC 1 57.891 11.032 72.297 1.00 0.00 MEMB O
> HETATM 5053 C22 POPC 1 57.151 13.320 71.994 1.00 0.00 MEMB C
> HETATM 5054 H2R POPC 1 57.401 13.932 72.891 1.00 0.00 MEMB H
> HETATM 5055 H2S POPC 1 56.187 13.680 71.592 1.00 0.00 MEMB H
> HETATM 5056 C3 POPC 1 55.468 9.317 73.407 1.00 0.00 MEMB C
> HETATM 5057 HX POPC 1 55.391 8.504 74.171 1.00 0.00 MEMB H
> HETATM 5058 HY POPC 1 56.158 8.966 72.609 1.00 0.00 MEMB H
> HETATM 5059 O31 POPC 1 54.187 9.694 72.868 1.00 0.00 MEMB O
> HETATM 5060 C31 POPC 1 53.224 8.795 72.812 1.00 0.00 MEMB C
> HETATM 5061 O32 POPC 1 53.329 7.608 73.007 1.00 0.00 MEMB O
> HETATM 5062 C32 POPC 1 51.893 9.478 72.615 1.00 0.00 MEMB C
> HETATM 5063 H2X POPC 1 52.092 10.482 72.205 1.00 0.00 MEMB H
> HETATM 5064 H2Y POPC 1 51.430 9.579 73.619 1.00 0.00 MEMB H
> HETATM 5065 C23 POPC 1 58.331 13.514 71.008 1.00 0.00 MEMB C
> HETATM 5066 H3R POPC 1 59.253 13.094 71.472 1.00 0.00 MEMB H
> HETATM 5067 H3S POPC 1 58.500 14.607 70.883 1.00 0.00 MEMB H
> HETATM 5068 C24 POPC 1 58.164 12.894 69.615 1.00 0.00 MEMB C
> HETATM 5069 H4R POPC 1 57.367 13.425 69.050 1.00 0.00 MEMB H
> HETATM 5070 H4S POPC 1 57.861 11.826 69.713 1.00 0.00 MEMB H
> HETATM 5071 C25 POPC 1 59.494 12.924 68.842 1.00 0.00 MEMB C
> HETATM 5072 H5R POPC 1 60.238 12.340 69.434 1.00 0.00 MEMB H
> HETATM 5073 H5S POPC 1 59.881 13.965 68.769 1.00 0.00 MEMB H
> HETATM 5074 C26 POPC 1 59.423 12.290 67.446 1.00 0.00 MEMB C
> HETATM 5075 H6R POPC 1 59.101 11.228 67.544 1.00 0.00 MEMB H
> HETATM 5076 H6S POPC 1 60.444 12.293 67.005 1.00 0.00 MEMB H
> HETATM 5077 C27 POPC 1 58.453 12.994 66.490 1.00 0.00 MEMB C
> HETATM 5078 H7R POPC 1 58.598 14.091 66.570 1.00 0.00 MEMB H
> HETATM 5079 H7S POPC 1 57.420 12.763 66.838 1.00 0.00 MEMB H
> HETATM 5080 C28 POPC 1 58.630 12.536 65.026 1.00 0.00 MEMB C
> HETATM 5081 H8R POPC 1 58.796 11.436 65.041 1.00 0.00 MEMB H
> HETATM 5082 H8S POPC 1 59.545 13.000 64.592 1.00 0.00 MEMB H
> HETATM 5083 C29 POPC 1 57.421 12.832 64.179 1.00 0.00 MEMB C
> HETATM 5084 H91 POPC 1 56.628 13.394 64.692 1.00 0.00 MEMB H
> HETATM 5085 C210 POPC 1 57.227 12.445 62.904 1.00 0.00 MEMB C
> HETATM 5086 H101 POPC 1 56.274 12.702 62.416 1.00 0.00 MEMB H
> HETATM 5087 C211 POPC 1 58.198 11.637 62.075 1.00 0.00 MEMB C
> HETATM 5088 H11R POPC 1 59.239 11.971 62.280 1.00 0.00 MEMB H
> HETATM 5089 H11S POPC 1 58.024 11.804 60.986 1.00 0.00 MEMB H
> HETATM 5090 C212 POPC 1 58.089 10.125 62.355 1.00 0.00 MEMB C
> HETATM 5091 H12R POPC 1 57.198 9.724 61.828 1.00 0.00 MEMB H
> HETATM 5092 H12S POPC 1 57.926 9.945 63.443 1.00 0.00 MEMB H
> HETATM 5093 C213 POPC 1 59.340 9.331 61.941 1.00 0.00 MEMB C
> HETATM 5094 H13R POPC 1 60.128 9.548 62.701 1.00 0.00 MEMB H
> HETATM 5095 H13S POPC 1 59.717 9.671 60.953 1.00 0.00 MEMB H
> HETATM 5096 C214 POPC 1 59.123 7.808 61.923 1.00 0.00 MEMB C
> HETATM 5097 H14R POPC 1 58.677 7.515 62.900 1.00 0.00 MEMB H
> HETATM 5098 H14S POPC 1 60.112 7.302 61.841 1.00 0.00 MEMB H
> HETATM 5099 C215 POPC 1 58.232 7.269 60.790 1.00 0.00 MEMB C
> HETATM 5100 H15R POPC 1 58.801 7.274 59.835 1.00 0.00 MEMB H
> HETATM 5101 H15S POPC 1 57.343 7.921 60.646 1.00 0.00 MEMB H
> HETATM 5102 C216 POPC 1 57.732 5.855 61.128 1.00 0.00 MEMB C
> HETATM 5103 H16R POPC 1 57.033 5.948 61.991 1.00 0.00 MEMB H
> HETATM 5104 H16S POPC 1 58.584 5.219 61.457 1.00 0.00 MEMB H
> HETATM 5105 C217 POPC 1 56.983 5.148 59.994 1.00 0.00 MEMB C
> HETATM 5106 H17R POPC 1 57.681 4.926 59.154 1.00 0.00 MEMB H
> HETATM 5107 H17S POPC 1 56.198 5.837 59.608 1.00 0.00 MEMB H
> HETATM 5108 C218 POPC 1 56.319 3.855 60.475 1.00 0.00 MEMB C
> HETATM 5109 H18R POPC 1 55.789 3.337 59.650 1.00 0.00 MEMB H
> HETATM 5110 H18S POPC 1 55.577 4.084 61.270 1.00 0.00 MEMB H
> HETATM 5111 H18T POPC 1 57.074 3.159 60.899 1.00 0.00 MEMB H
> HETATM 5112 C33 POPC 1 50.927 8.722 71.681 1.00 0.00 MEMB C
> HETATM 5113 H3X POPC 1 50.627 7.741 72.105 1.00 0.00 MEMB H
> HETATM 5114 H3Y POPC 1 51.417 8.528 70.700 1.00 0.00 MEMB H
> HETATM 5115 C34 POPC 1 49.665 9.557 71.448 1.00 0.00 MEMB C
> HETATM 5116 H4X POPC 1 49.976 10.507 70.960 1.00 0.00 MEMB H
> HETATM 5117 H4Y POPC 1 49.203 9.817 72.427 1.00 0.00 MEMB H
> HETATM 5118 C35 POPC 1 48.624 8.838 70.580 1.00 0.00 MEMB C
> HETATM 5119 H5X POPC 1 47.960 8.220 71.227 1.00 0.00 MEMB H
> HETATM 5120 H5Y POPC 1 49.163 8.147 69.893 1.00 0.00 MEMB H
> HETATM 5121 C36 POPC 1 47.791 9.815 69.738 1.00 0.00 MEMB C
> HETATM 5122 H6X POPC 1 48.442 10.662 69.417 1.00 0.00 MEMB H
> HETATM 5123 H6Y POPC 1 46.991 10.251 70.375 1.00 0.00 MEMB H
> HETATM 5124 C37 POPC 1 47.196 9.177 68.469 1.00 0.00 MEMB C
> HETATM 5125 H7X POPC 1 46.219 9.668 68.262 1.00 0.00 MEMB H
> HETATM 5126 H7Y POPC 1 46.993 8.096 68.646 1.00 0.00 MEMB H
> HETATM 5127 C38 POPC 1 48.116 9.378 67.244 1.00 0.00 MEMB C
> HETATM 5128 H8X POPC 1 49.021 8.751 67.373 1.00 0.00 MEMB H
> HETATM 5129 H8Y POPC 1 48.440 10.443 67.239 1.00 0.00 MEMB H
> HETATM 5130 C39 POPC 1 47.449 9.077 65.886 1.00 0.00 MEMB C
> HETATM 5131 H9X POPC 1 46.509 9.661 65.842 1.00 0.00 MEMB H
> HETATM 5132 H9Y POPC 1 47.180 8.000 65.849 1.00 0.00 MEMB H
> HETATM 5133 C310 POPC 1 48.303 9.446 64.653 1.00 0.00 MEMB C
> HETATM 5134 H10X POPC 1 49.346 9.097 64.826 1.00 0.00 MEMB H
> HETATM 5135 H10Y POPC 1 48.345 10.552 64.547 1.00 0.00 MEMB H
> HETATM 5136 C311 POPC 1 47.820 8.851 63.312 1.00 0.00 MEMB C
> HETATM 5137 H11X POPC 1 47.764 7.747 63.378 1.00 0.00 MEMB H
> HETATM 5138 H11Y POPC 1 48.581 9.099 62.537 1.00 0.00 MEMB H
> HETATM 5139 C312 POPC 1 46.452 9.351 62.828 1.00 0.00 MEMB C
> HETATM 5140 H12X POPC 1 46.278 10.381 63.199 1.00 0.00 MEMB H
> HETATM 5141 H12Y POPC 1 45.653 8.706 63.259 1.00 0.00 MEMB H
> HETATM 5142 C313 POPC 1 46.317 9.373 61.295 1.00 0.00 MEMB C
> HETATM 5143 H13X POPC 1 46.485 8.349 60.898 1.00 0.00 MEMB H
> HETATM 5144 H13Y POPC 1 47.098 10.044 60.868 1.00 0.00 MEMB H
> HETATM 5145 C314 POPC 1 44.923 9.864 60.874 1.00 0.00 MEMB C
> HETATM 5146 H14X POPC 1 44.802 10.901 61.261 1.00 0.00 MEMB H
> HETATM 5147 H14Y POPC 1 44.159 9.225 61.373 1.00 0.00 MEMB H
> HETATM 5148 C315 POPC 1 44.653 9.865 59.361 1.00 0.00 MEMB C
> HETATM 5149 H15X POPC 1 44.467 8.820 59.020 1.00 0.00 MEMB H
> HETATM 5150 H15Y POPC 1 45.561 10.230 58.830 1.00 0.00 MEMB H
> HETATM 5151 C316 POPC 1 43.462 10.751 58.970 1.00 0.00 MEMB C
> HETATM 5152 H16X POPC 1 42.514 10.351 59.388 1.00 0.00 MEMB H
> HETATM 5153 H16Y POPC 1 43.358 10.819 57.866 1.00 0.00 MEMB H
> HETATM 5154 H16Z POPC 1 43.606 11.778 59.370 1.00 0.00 MEMB H
>
> That is amber output
> HETATM 42 C12 PA 1 51.893 9.478 72.615 1.00 0.00 MEMB C
> HETATM 43 H2R PA 1 52.092 10.482 72.205 1.00 0.00 MEMB H
> HETATM 44 H2S PA 1 51.430 9.579 73.619 1.00 0.00 MEMB H
> HETATM 92 C13 PA 1 50.927 8.722 71.681 1.00 0.00 MEMB C
> HETATM 93 H3R PA 1 50.627 7.741 72.105 1.00 0.00 MEMB H
> HETATM 94 H3S PA 1 51.417 8.528 70.700 1.00 0.00 MEMB H
> HETATM 95 C14 PA 1 49.665 9.557 71.448 1.00 0.00 MEMB C
> HETATM 96 H4R PA 1 49.976 10.507 70.960 1.00 0.00 MEMB H
> HETATM 97 H4S PA 1 49.203 9.817 72.427 1.00 0.00 MEMB H
> HETATM 98 C15 PA 1 48.624 8.838 70.580 1.00 0.00 MEMB C
> HETATM 99 H5R PA 1 47.960 8.220 71.227 1.00 0.00 MEMB H
> HETATM 100 H5S PA 1 49.163 8.147 69.893 1.00 0.00 MEMB H
> HETATM 101 C16 PA 1 47.791 9.815 69.738 1.00 0.00 MEMB C
> HETATM 102 H6R PA 1 48.442 10.662 69.417 1.00 0.00 MEMB H
> HETATM 103 H6S PA 1 46.991 10.251 70.375 1.00 0.00 MEMB H
> HETATM 104 C17 PA 1 47.196 9.177 68.469 1.00 0.00 MEMB C
> HETATM 105 H7R PA 1 46.219 9.668 68.262 1.00 0.00 MEMB H
> HETATM 106 H7S PA 1 46.993 8.096 68.646 1.00 0.00 MEMB H
> HETATM 107 C18 PA 1 48.116 9.378 67.244 1.00 0.00 MEMB C
> HETATM 108 H8R PA 1 49.021 8.751 67.373 1.00 0.00 MEMB H
> HETATM 109 H8S PA 1 48.440 10.443 67.239 1.00 0.00 MEMB H
> HETATM 110 C19 PA 1 47.449 9.077 65.886 1.00 0.00 MEMB C
> HETATM 111 H9R PA 1 46.509 9.661 65.842 1.00 0.00 MEMB H
> HETATM 112 H9S PA 1 47.180 8.000 65.849 1.00 0.00 MEMB H
> HETATM 113 C110 PA 1 48.303 9.446 64.653 1.00 0.00 MEMB C
> HETATM 114 H10R PA 1 49.346 9.097 64.826 1.00 0.00 MEMB H
> HETATM 115 H10S PA 1 48.345 10.552 64.547 1.00 0.00 MEMB H
> HETATM 116 C111 PA 1 47.820 8.851 63.312 1.00 0.00 MEMB C
> HETATM 117 H11R PA 1 47.764 7.747 63.378 1.00 0.00 MEMB H
> HETATM 118 H11S PA 1 48.581 9.099 62.537 1.00 0.00 MEMB H
> HETATM 119 C112 PA 1 46.452 9.351 62.828 1.00 0.00 MEMB C
> HETATM 120 H12R PA 1 46.278 10.381 63.199 1.00 0.00 MEMB H
> HETATM 121 H12S PA 1 45.653 8.706 63.259 1.00 0.00 MEMB H
> HETATM 122 C113 PA 1 46.317 9.373 61.295 1.00 0.00 MEMB C
> HETATM 123 H13R PA 1 46.485 8.349 60.898 1.00 0.00 MEMB H
> HETATM 124 H13S PA 1 47.098 10.044 60.868 1.00 0.00 MEMB H
> HETATM 125 C114 PA 1 44.923 9.864 60.874 1.00 0.00 MEMB C
> HETATM 126 H14R PA 1 44.802 10.901 61.261 1.00 0.00 MEMB H
> HETATM 127 H14S PA 1 44.159 9.225 61.373 1.00 0.00 MEMB H
> HETATM 128 C115 PA 1 44.653 9.865 59.361 1.00 0.00 MEMB C
> HETATM 129 H15R PA 1 44.467 8.820 59.020 1.00 0.00 MEMB H
> HETATM 130 H15S PA 1 45.561 10.230 58.830 1.00 0.00 MEMB H
> HETATM 131 C116 PA 1 43.462 10.751 58.970 1.00 0.00 MEMB C
> HETATM 132 H16R PA 1 42.514 10.351 59.388 1.00 0.00 MEMB H
> HETATM 133 H16S PA 1 43.358 10.819 57.866 1.00 0.00 MEMB H
> HETATM 134 H16T PA 1 43.606 11.778 59.370 1.00 0.00 MEMB H
> HETATM 1 N31 PC 1 61.437 11.706 76.909 1.00 0.00 MEMB N
> HETATM 2 C32 PC 1 60.270 12.523 76.385 1.00 0.00 MEMB C
> HETATM 3 H2A PC 1 60.666 13.234 75.669 1.00 0.00 MEMB H
> HETATM 4 H2B PC 1 59.904 13.131 77.217 1.00 0.00 MEMB H
> HETATM 5 C33 PC 1 62.013 10.785 75.885 1.00 0.00 MEMB C
> HETATM 6 H3A PC 1 62.438 11.312 75.036 1.00 0.00 MEMB H
> HETATM 7 H3B PC 1 62.825 10.206 76.317 1.00 0.00 MEMB H
> HETATM 8 H3C PC 1 61.275 10.086 75.513 1.00 0.00 MEMB H
> HETATM 9 C34 PC 1 62.511 12.640 77.320 1.00 0.00 MEMB C
> HETATM 10 H4A PC 1 62.944 13.114 76.446 1.00 0.00 MEMB H
> HETATM 11 H4B PC 1 62.110 13.448 77.926 1.00 0.00 MEMB H
> HETATM 12 H4C PC 1 63.293 12.118 77.844 1.00 0.00 MEMB H
> HETATM 13 C35 PC 1 60.956 10.903 78.081 1.00 0.00 MEMB C
> HETATM 14 H5A PC 1 60.724 11.540 78.924 1.00 0.00 MEMB H
> HETATM 15 H5B PC 1 61.698 10.182 78.389 1.00 0.00 MEMB H
> HETATM 16 H5C PC 1 60.042 10.371 77.808 1.00 0.00 MEMB H
> HETATM 17 C31 PC 1 59.042 11.806 75.756 1.00 0.00 MEMB C
> HETATM 18 H1A PC 1 59.405 11.262 74.850 1.00 0.00 MEMB H
> HETATM 19 H1B PC 1 58.355 12.595 75.363 1.00 0.00 MEMB H
> HETATM 20 P31 PC 1 57.053 11.363 77.439 1.00 0.00 MEMB P
> HETATM 21 O33 PC 1 57.452 12.587 78.178 1.00 0.00 MEMB O
> HETATM 22 O34 PC 1 56.546 10.245 78.289 1.00 0.00 MEMB O
> HETATM 23 O32 PC 1 58.374 10.902 76.663 1.00 0.00 MEMB O
> HETATM 24 O31 PC 1 56.037 11.754 76.295 1.00 0.00 MEMB O
> HETATM 25 C3 PC 1 55.362 10.795 75.477 1.00 0.00 MEMB C
> HETATM 26 HA PC 1 54.345 11.170 75.235 1.00 0.00 MEMB H
> HETATM 27 HB PC 1 55.222 9.815 75.992 1.00 0.00 MEMB H
> HETATM 28 C2 PC 1 56.094 10.548 74.132 1.00 0.00 MEMB C
> HETATM 29 HX PC 1 57.145 10.281 74.404 1.00 0.00 MEMB H
> HETATM 30 O21 PC 1 56.015 11.762 73.320 1.00 0.00 MEMB O
> HETATM 31 C21 PC 1 57.036 11.881 72.487 1.00 0.00 MEMB C
> HETATM 32 O22 PC 1 57.891 11.032 72.297 1.00 0.00 MEMB O
> HETATM 36 C1 PC 1 55.468 9.317 73.407 1.00 0.00 MEMB C
> HETATM 37 HR PC 1 55.391 8.504 74.171 1.00 0.00 MEMB H
> HETATM 38 HS PC 1 56.158 8.966 72.609 1.00 0.00 MEMB H
> HETATM 39 O11 PC 1 54.187 9.694 72.868 1.00 0.00 MEMB O
> HETATM 40 C11 PC 1 53.224 8.795 72.812 1.00 0.00 MEMB C
> HETATM 41 O12 PC 1 53.329 7.608 73.007 1.00 0.00 MEMB O
> HETATM 33 C12 OL 1 57.151 13.320 71.994 1.00 0.00 MEMB C
> HETATM 34 H2R OL 1 57.401 13.932 72.891 1.00 0.00 MEMB H
> HETATM 35 H2S OL 1 56.187 13.680 71.592 1.00 0.00 MEMB H
> HETATM 45 C13 OL 1 58.331 13.514 71.008 1.00 0.00 MEMB C
> HETATM 46 H3R OL 1 59.253 13.094 71.472 1.00 0.00 MEMB H
> HETATM 47 H3S OL 1 58.500 14.607 70.883 1.00 0.00 MEMB H
> HETATM 48 C14 OL 1 58.164 12.894 69.615 1.00 0.00 MEMB C
> HETATM 49 H4R OL 1 57.367 13.425 69.050 1.00 0.00 MEMB H
> HETATM 50 H4S OL 1 57.861 11.826 69.713 1.00 0.00 MEMB H
> HETATM 51 C15 OL 1 59.494 12.924 68.842 1.00 0.00 MEMB C
> HETATM 52 H5R OL 1 60.238 12.340 69.434 1.00 0.00 MEMB H
> HETATM 53 H5S OL 1 59.881 13.965 68.769 1.00 0.00 MEMB H
> HETATM 54 C16 OL 1 59.423 12.290 67.446 1.00 0.00 MEMB C
> HETATM 55 H6R OL 1 59.101 11.228 67.544 1.00 0.00 MEMB H
> HETATM 56 H6S OL 1 60.444 12.293 67.005 1.00 0.00 MEMB H
> HETATM 57 C17 OL 1 58.453 12.994 66.490 1.00 0.00 MEMB C
> HETATM 58 H7R OL 1 58.598 14.091 66.570 1.00 0.00 MEMB H
> HETATM 59 H7S OL 1 57.420 12.763 66.838 1.00 0.00 MEMB H
> HETATM 60 C18 OL 1 58.630 12.536 65.026 1.00 0.00 MEMB C
> HETATM 61 H8R OL 1 58.796 11.436 65.041 1.00 0.00 MEMB H
> HETATM 62 H8S OL 1 59.545 13.000 64.592 1.00 0.00 MEMB H
> HETATM 63 C19 OL 1 57.421 12.832 64.179 1.00 0.00 MEMB C
> HETATM 64 H9R OL 1 56.628 13.394 64.692 1.00 0.00 MEMB H
> HETATM 65 C110 OL 1 57.227 12.445 62.904 1.00 0.00 MEMB C
> HETATM 66 H10R OL 1 56.274 12.702 62.416 1.00 0.00 MEMB H
> HETATM 67 C111 OL 1 58.198 11.637 62.075 1.00 0.00 MEMB C
> HETATM 68 H11R OL 1 59.239 11.971 62.280 1.00 0.00 MEMB H
> HETATM 69 H11S OL 1 58.024 11.804 60.986 1.00 0.00 MEMB H
> HETATM 70 C112 OL 1 58.089 10.125 62.355 1.00 0.00 MEMB C
> HETATM 71 H12R OL 1 57.198 9.724 61.828 1.00 0.00 MEMB H
> HETATM 72 H12S OL 1 57.926 9.945 63.443 1.00 0.00 MEMB H
> HETATM 73 C113 OL 1 59.340 9.331 61.941 1.00 0.00 MEMB C
> HETATM 74 H13R OL 1 60.128 9.548 62.701 1.00 0.00 MEMB H
> HETATM 75 H13S OL 1 59.717 9.671 60.953 1.00 0.00 MEMB H
> HETATM 76 C114 OL 1 59.123 7.808 61.923 1.00 0.00 MEMB C
> HETATM 77 H14R OL 1 58.677 7.515 62.900 1.00 0.00 MEMB H
> HETATM 78 H14S OL 1 60.112 7.302 61.841 1.00 0.00 MEMB H
> HETATM 79 C115 OL 1 58.232 7.269 60.790 1.00 0.00 MEMB C
> HETATM 80 H15R OL 1 58.801 7.274 59.835 1.00 0.00 MEMB H
> HETATM 81 H15S OL 1 57.343 7.921 60.646 1.00 0.00 MEMB H
> HETATM 82 C116 OL 1 57.732 5.855 61.128 1.00 0.00 MEMB C
> HETATM 83 H16R OL 1 57.033 5.948 61.991 1.00 0.00 MEMB H
> HETATM 84 H16S OL 1 58.584 5.219 61.457 1.00 0.00 MEMB H
> HETATM 85 C117 OL 1 56.983 5.148 59.994 1.00 0.00 MEMB C
> HETATM 86 H17R OL 1 57.681 4.926 59.154 1.00 0.00 MEMB H
> HETATM 87 H17S OL 1 56.198 5.837 59.608 1.00 0.00 MEMB H
> HETATM 88 C118 OL 1 56.319 3.855 60.475 1.00 0.00 MEMB C
> HETATM 89 H18R OL 1 55.789 3.337 59.650 1.00 0.00 MEMB H
> HETATM 90 H18S OL 1 55.577 4.084 61.270 1.00 0.00 MEMB H
> HETATM 91 H18T OL 1 57.074 3.159 60.899 1.00 0.00 MEMB H
>
> A question: is it normal that the lipid now is separated onto the 3
> different specifies ? :) The tleap send me the warnings:
>
> Warning: name change in pdb file residue 7 ;
> this residue is split into PA and PC.
> Warning: name change in pdb file residue 7 ;
> this residue is split into PC and OL.
>
> and the resulting system is look like:
> OL 120
> PA 120
> PC 120
> WAT 10754
>
> Thanks for the help!
>
> james
>
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Received on Wed Aug 16 2017 - 11:30:03 PDT
