AMBER Archive (2009)

Subject: [AMBER] How to obtain amber top and crd from pdb file with POPE lipids?

From: decastro_at_physics.usyd.edu.au
Date: Sun Sep 27 2009 - 23:52:20 CDT

Dear all,

We would like to do some MD simulations for membranes. We have a big
amount of lipids (POPE as written in the pdb file) but I can not find
a way to obtain the amber topology and coordinate files with
xleap/tleap in first place. It seems to be that amber is not reading
the corresponding POPE lines from the .pdb file. I went through the
amber .lib files in oder to have some hint about how to edit the .pdb
file, but I can not find anything there about the lipids.

Here I copy below some of the lines form the .pdb file we suppose we
should change (one residue). The question is if somebody knows how to
change these lines in order to have a pdb file readable with amber?

Thanks in advance for any feedback!

Regards, Alex

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ATOM 6297 N POPEP 1 -31.006 -25.247 18.731 0.00 0.00 POPE
ATOM 6298 HN1 POPEP 1 -30.054 -24.839 18.638 0.00 0.00 POPE
ATOM 6299 HN2 POPEP 1 -31.091 -26.200 19.139 0.00 0.00 POPE
ATOM 6300 HN3 POPEP 1 -31.437 -25.233 17.784 0.00 0.00 POPE
ATOM 6301 C12 POPEP 1 -31.683 -24.282 19.701 0.00 0.00 POPE
ATOM 6302 H12A POPEP 1 -30.857 -24.069 20.412 0.00 0.00 POPE
ATOM 6303 H12B POPEP 1 -32.605 -24.667 20.187 0.00 0.00 POPE
ATOM 6304 C11 POPEP 1 -31.953 -23.314 18.655 0.00 0.00 POPE
ATOM 6305 H11A POPEP 1 -32.922 -23.487 18.140 0.00 0.00 POPE
ATOM 6306 H11B POPEP 1 -31.905 -22.250 18.972 0.00 0.00 POPE
ATOM 6307 P POPEP 1 -30.947 -22.420 16.632 0.00 0.00 POPE
ATOM 6308 O13 POPEP 1 -32.165 -21.611 16.835 0.00 0.00 POPE
ATOM 6309 O14 POPEP 1 -29.693 -21.667 16.783 0.00 0.00 POPE
ATOM 6310 O11 POPEP 1 -30.981 -23.047 15.262 0.00 0.00 POPE
ATOM 6311 O12 POPEP 1 -30.944 -23.655 17.652 0.00 0.00 POPE
ATOM 6312 C1 POPEP 1 -29.653 -23.558 15.020 0.00 0.00 POPE
ATOM 6313 HA POPEP 1 -29.064 -22.681 14.676 0.00 0.00 POPE
ATOM 6314 HB POPEP 1 -29.196 -23.964 15.948 0.00 0.00 POPE
ATOM 6315 C2 POPEP 1 -29.684 -24.694 14.070 0.00 0.00 POPE
ATOM 6316 HS POPEP 1 -28.802 -24.859 13.415 0.00 0.00 POPE
ATOM 6317 O21 POPEP 1 -30.877 -24.634 13.346 0.00 0.00 POPE
ATOM 6318 C21 POPEP 1 -30.747 -24.138 12.086 0.00 0.00 POPE
ATOM 6319 O22 POPEP 1 -29.695 -23.700 11.613 0.00 0.00 POPE
ATOM 6320 C22 POPEP 1 -32.065 -24.370 11.366 0.00 0.00 POPE
ATOM 6321 H2R POPEP 1 -32.661 -25.109 11.944 0.00 0.00 POPE
ATOM 6322 H2S POPEP 1 -32.610 -23.418 11.543 0.00 0.00 POPE
ATOM 6323 C3 POPEP 1 -29.766 -26.102 14.706 0.00 0.00 POPE
ATOM 6324 HX POPEP 1 -28.758 -26.544 14.858 0.00 0.00 POPE
ATOM 6325 HY POPEP 1 -30.151 -26.009 15.744 0.00 0.00 POPE
ATOM 6326 O31 POPEP 1 -30.604 -26.982 13.911 0.00 0.00 POPE
ATOM 6327 C31 POPEP 1 -30.681 -28.183 14.342 0.00 0.00 POPE
ATOM 6328 O32 POPEP 1 -30.203 -28.672 15.341 0.00 0.00 POPE
ATOM 6329 C32 POPEP 1 -31.515 -28.910 13.295 0.00 0.00 POPE
ATOM 6330 H2X POPEP 1 -31.542 -29.995 13.530 0.00 0.00 POPE
ATOM 6331 H2Y POPEP 1 -32.592 -28.653 13.382 0.00 0.00 POPE
ATOM 6332 C23 POPEP 1 -31.738 -24.665 9.947 0.00 0.00 POPE
ATOM 6333 H3R POPEP 1 -31.223 -23.810 9.459 0.00 0.00 POPE
ATOM 6334 H3S POPEP 1 -31.116 -25.582 9.864 0.00 0.00 POPE
ATOM 6335 C24 POPEP 1 -32.923 -25.007 8.980 0.00 0.00 POPE
ATOM 6336 H4R POPEP 1 -33.714 -24.229 9.038 0.00 0.00 POPE
ATOM 6337 H4S POPEP 1 -32.493 -24.757 7.987 0.00 0.00 POPE
ATOM 6338 C25 POPEP 1 -33.649 -26.331 9.140 0.00 0.00 POPE
ATOM 6339 H5R POPEP 1 -33.041 -27.127 8.659 0.00 0.00 POPE
ATOM 6340 H5S POPEP 1 -33.892 -26.533 10.205 0.00 0.00 POPE
ATOM 6341 C26 POPEP 1 -35.114 -26.368 8.482 0.00 0.00 POPE
ATOM 6342 H6R POPEP 1 -35.538 -27.331 8.837 0.00 0.00 POPE
ATOM 6343 H6S POPEP 1 -35.692 -25.571 8.996 0.00 0.00 POPE
ATOM 6344 C27 POPEP 1 -35.202 -26.181 6.953 0.00 0.00 POPE
ATOM 6345 H7R POPEP 1 -36.224 -26.275 6.529 0.00 0.00 POPE
ATOM 6346 H7S POPEP 1 -34.963 -25.168 6.565 0.00 0.00 POPE
ATOM 6347 C28 POPEP 1 -34.294 -27.072 6.126 0.00 0.00 POPE
ATOM 6348 H8R POPEP 1 -34.533 -26.857 5.063 0.00 0.00 POPE
ATOM 6349 H8S POPEP 1 -33.244 -26.821 6.389 0.00 0.00 POPE
ATOM 6350 C29 POPEP 1 -34.411 -28.580 6.416 0.00 0.00 POPE
ATOM 6351 H91 POPEP 1 -33.975 -28.900 7.374 0.00 0.00 POPE
ATOM 6352 C210 POPEP 1 -34.948 -29.485 5.557 0.00 0.00 POPE
ATOM 6353 H101 POPEP 1 -34.951 -30.521 5.926 0.00 0.00 POPE
ATOM 6354 C211 POPEP 1 -35.574 -29.226 4.257 0.00 0.00 POPE
ATOM 6355 H11R POPEP 1 -36.650 -29.502 4.274 0.00 0.00 POPE
ATOM 6356 H11S POPEP 1 -35.627 -28.180 3.887 0.00 0.00 POPE
ATOM 6357 C212 POPEP 1 -34.789 -29.936 3.152 0.00 0.00 POPE
ATOM 6358 H12R POPEP 1 -33.697 -29.741 3.094 0.00 0.00 POPE
ATOM 6359 H12S POPEP 1 -34.772 -30.963 3.575 0.00 0.00 POPE
ATOM 6360 C213 POPEP 1 -35.387 -29.844 1.844 0.00 0.00 POPE
ATOM 6361 H13R POPEP 1 -34.843 -30.662 1.324 0.00 0.00 POPE
ATOM 6362 H13S POPEP 1 -36.463 -30.112 1.910 0.00 0.00 POPE
ATOM 6363 C214 POPEP 1 -35.189 -28.494 1.192 0.00 0.00 POPE
ATOM 6364 H14R POPEP 1 -35.547 -28.218 0.177 0.00 0.00 POPE
ATOM 6365 H14S POPEP 1 -35.708 -27.817 1.904 0.00 0.00 POPE
ATOM 6366 C215 POPEP 1 -33.723 -27.921 1.090 0.00 0.00 POPE
ATOM 6367 H15R POPEP 1 -33.709 -26.876 0.713 0.00 0.00 POPE
ATOM 6368 H15S POPEP 1 -33.461 -27.830 2.166 0.00 0.00 POPE
ATOM 6369 C216 POPEP 1 -32.544 -28.759 0.440 0.00 0.00 POPE
ATOM 6370 H16R POPEP 1 -31.650 -28.330 0.941 0.00 0.00 POPE
ATOM 6371 H16S POPEP 1 -32.511 -29.842 0.686 0.00 0.00 POPE
ATOM 6372 C217 POPEP 1 -32.616 -28.635 -1.079 0.00 0.00 POPE
ATOM 6373 H17R POPEP 1 -33.633 -28.921 -1.426 0.00 0.00 POPE
ATOM 6374 H17S POPEP 1 -32.468 -27.571 -1.361 0.00 0.00 POPE
ATOM 6375 C218 POPEP 1 -31.696 -29.559 -1.871 0.00 0.00 POPE
ATOM 6376 H18R POPEP 1 -31.906 -30.639 -1.717 0.00 0.00 POPE
ATOM 6377 H18S POPEP 1 -31.986 -29.302 -2.913 0.00 0.00 POPE
ATOM 6378 H18T POPEP 1 -30.620 -29.358 -1.680 0.00 0.00 POPE
ATOM 6379 C33 POPEP 1 -30.838 -28.700 11.915 0.00 0.00 POPE
ATOM 6380 H3X POPEP 1 -30.426 -27.694 11.687 0.00 0.00 POPE
ATOM 6381 H3Y POPEP 1 -29.923 -29.330 11.903 0.00 0.00 POPE
ATOM 6382 C34 POPEP 1 -31.817 -29.071 10.796 0.00 0.00 POPE
ATOM 6383 H4X POPEP 1 -32.017 -30.163 10.815 0.00 0.00 POPE
ATOM 6384 H4Y POPEP 1 -32.814 -28.581 10.816 0.00 0.00 POPE
ATOM 6385 C35 POPEP 1 -31.219 -28.857 9.397 0.00 0.00 POPE
ATOM 6386 H5X POPEP 1 -31.978 -29.171 8.649 0.00 0.00 POPE
ATOM 6387 H5Y POPEP 1 -31.159 -27.751 9.300 0.00 0.00 POPE
ATOM 6388 C36 POPEP 1 -29.885 -29.508 9.053 0.00 0.00 POPE
ATOM 6389 H6X POPEP 1 -29.008 -29.130 9.620 0.00 0.00 POPE
ATOM 6390 H6Y POPEP 1 -30.070 -30.576 9.295 0.00 0.00 POPE
ATOM 6391 C37 POPEP 1 -29.403 -29.442 7.544 0.00 0.00 POPE
ATOM 6392 H7X POPEP 1 -28.790 -28.516 7.571 0.00 0.00 POPE
ATOM 6393 H7Y POPEP 1 -28.852 -30.406 7.502 0.00 0.00 POPE
ATOM 6394 C38 POPEP 1 -30.473 -29.362 6.434 0.00 0.00 POPE
ATOM 6395 H8X POPEP 1 -31.319 -30.077 6.525 0.00 0.00 POPE
ATOM 6396 H8Y POPEP 1 -30.906 -28.341 6.367 0.00 0.00 POPE
ATOM 6397 C39 POPEP 1 -29.866 -29.525 5.056 0.00 0.00 POPE
ATOM 6398 H9X POPEP 1 -30.473 -29.124 4.216 0.00 0.00 POPE
ATOM 6399 H9Y POPEP 1 -28.840 -29.099 5.053 0.00 0.00 POPE
ATOM 6400 C310 POPEP 1 -29.566 -30.994 4.651 0.00 0.00 POPE
ATOM 6401 H10X POPEP 1 -29.351 -31.082 3.565 0.00 0.00 POPE
ATOM 6402 H10Y POPEP 1 -28.734 -31.374 5.282 0.00 0.00 POPE
ATOM 6403 C311 POPEP 1 -30.679 -32.066 4.886 0.00 0.00 POPE
ATOM 6404 H11X POPEP 1 -30.225 -33.035 4.588 0.00 0.00 POPE
ATOM 6405 H11Y POPEP 1 -30.929 -32.169 5.964 0.00 0.00 POPE
ATOM 6406 C312 POPEP 1 -31.949 -31.793 4.052 0.00 0.00 POPE
ATOM 6407 H12X POPEP 1 -32.721 -32.565 4.256 0.00 0.00 POPE
ATOM 6408 H12Y POPEP 1 -32.516 -30.884 4.346 0.00 0.00 POPE
ATOM 6409 C313 POPEP 1 -31.665 -31.744 2.533 0.00 0.00 POPE
ATOM 6410 H13X POPEP 1 -32.633 -31.558 2.021 0.00 0.00 POPE
ATOM 6411 H13Y POPEP 1 -31.027 -30.847 2.383 0.00 0.00 POPE
ATOM 6412 C314 POPEP 1 -31.029 -32.996 1.956 0.00 0.00 POPE
ATOM 6413 H14X POPEP 1 -30.680 -32.859 0.910 0.00 0.00 POPE
ATOM 6414 H14Y POPEP 1 -30.093 -33.008 2.553 0.00 0.00 POPE
ATOM 6415 C315 POPEP 1 -31.750 -34.370 2.159 0.00 0.00 POPE
ATOM 6416 H15X POPEP 1 -31.067 -35.094 1.666 0.00 0.00 POPE
ATOM 6417 H15Y POPEP 1 -31.801 -34.654 3.232 0.00 0.00 POPE
ATOM 6418 C316 POPEP 1 -33.053 -34.363 1.484 0.00 0.00 POPE
ATOM 6419 H16X POPEP 1 -33.007 -34.008 0.432 0.00 0.00 POPE
ATOM 6420 H16Y POPEP 1 -33.580 -35.341 1.470 0.00 0.00 POPE
ATOM 6421 H16Z POPEP 1 -33.713 -33.664 2.040 0.00 0.00 POPE

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