Hello:
I think I may found the problem: in the popc.itp of Slipid FF, there
are 134 atoms defined. However, there are only 116 atoms in the file
generated by charmm-GUI. And I found that it is not POPC, but POPA,
although I asked for POPC when I proceed online (checked from my cookie).
ATOM 6309 P POPA 22 -15.804 13.129 19.464 1.00-18.71 MEMB
ATOM 6310 O13 POPA 22 -15.836 12.049 20.465 1.00-18.68 MEMB
ATOM 6311 O14 POPA 22 -15.558 14.510 19.908 1.00-18.60 MEMB
ATOM 6312 O12 POPA 22 -17.279 13.180 18.915 1.00 0.00 MEMB
ATOM 6313 H12 POPA 22 -17.836 13.469 19.643 1.00 0.00 MEMB
ATOM 6314 O11 POPA 22 -14.915 12.749 18.217 1.00-17.32 MEMB
ATOM 6315 C1 POPA 22 -14.766 13.647 17.113 1.00-16.12 MEMB
ATOM 6316 HA POPA 22 -13.736 14.067 17.124 1.00 0.00 MEMB
ATOM 6317 HB POPA 22 -15.471 14.513 17.143 1.00 0.00 MEMB
ATOM 6318 C2 POPA 22 -14.986 12.875 15.787 1.00-15.10 MEMB
ATOM 6319 HS POPA 22 -15.193 11.816 16.082 1.00 0.00 MEMB
ATOM 6320 O21 POPA 22 -13.785 12.941 14.994 1.00-14.07 MEMB
ATOM 6321 C21 POPA 22 -13.670 11.983 14.087 1.00-13.35 MEMB
ATOM 6322 O22 POPA 22 -14.477 11.093 13.884 1.00-13.62 MEMB
ATOM 6323 C22 POPA 22 -12.330 12.149 13.368 1.00-12.06 MEMB
ATOM 6324 H2R POPA 22 -11.520 12.013 14.114 1.00 0.00 MEMB
ATOM 6325 H2S POPA 22 -12.292 13.193 12.997 1.00 0.00 MEMB
ATOM 6326 C3 POPA 22 -16.240 13.384 15.014 1.00-14.49 MEMB
ATOM 6327 HX POPA 22 -17.103 13.231 15.701 1.00 0.00 MEMB
ATOM 6328 HY POPA 22 -16.426 12.735 14.128 1.00 0.00 MEMB
ATOM 6329 O31 POPA 22 -16.173 14.793 14.692 1.00-13.57 MEMB
ATOM 6330 C31 POPA 22 -15.882 15.097 13.431 1.00-13.15 MEMB
ATOM 6331 O32 POPA 22 -15.612 14.299 12.552 1.00-13.67 MEMB
ATOM 6332 C32 POPA 22 -15.981 16.618 13.234 1.00-11.81 MEMB
ATOM 6333 H2X POPA 22 -14.965 17.021 13.404 1.00 0.00 MEMB
ATOM 6334 H2Y POPA 22 -16.629 17.049 14.013 1.00 0.00 MEMB
ATOM 6335 C23 POPA 22 -12.145 11.147 12.203 1.00-10.86 MEMB
ATOM 6336 H3R POPA 22 -13.002 11.251 11.497 1.00 0.00 MEMB
ATOM 6337 H3S POPA 22 -12.165 10.105 12.597 1.00 0.00 MEMB
ATOM 6338 C24 POPA 22 -10.842 11.358 11.408 1.00-10.31 MEMB
ATOM 6339 H4R POPA 22 -10.828 10.635 10.562 1.00 0.00 MEMB
ATOM 6340 H4S POPA 22 -9.965 11.139 12.055 1.00 0.00 MEMB
ATOM 6341 C25 POPA 22 -10.721 12.786 10.858 1.00 -8.77
MEMB
ATOM 6342 H5R POPA 22 -10.532 13.482 11.706 1.00 0.00 MEMB
ATOM 6343 H5S POPA 22 -11.700 13.052 10.409 1.00 0.00 MEMB
ATOM 6344 C26 POPA 22 -9.628 13.004 9.802 1.00 -8.20
MEMB
ATOM 6345 H6R POPA 22 -8.667 12.568 10.149 1.00 0.00 MEMB
ATOM 6346 H6S POPA 22 -9.478 14.104 9.696 1.00 0.00 MEMB
ATOM 6347 C27 POPA 22 -9.994 12.452 8.415 1.00 -7.26
MEMB
ATOM 6348 H7R POPA 22 -11.033 12.767 8.167 1.00 0.00 MEMB
ATOM 6349 H7S POPA 22 -9.974 11.339 8.451 1.00 0.00 MEMB
ATOM 6350 C28 POPA 22 -9.039 12.966 7.320 1.00 -6.58
MEMB
ATOM 6351 H8R POPA 22 -8.001 12.690 7.614 1.00 0.00 MEMB
ATOM 6352 H8S POPA 22 -9.092 14.077 7.305 1.00 0.00 MEMB
ATOM 6353 C29 POPA 22 -9.367 12.419 5.955 1.00 -5.84
MEMB
ATOM 6354 H91 POPA 22 -10.320 11.873 5.877 1.00 0.00 MEMB
ATOM 6355 C210 POPA 22 -8.591 12.542 4.862 1.00 -4.56
MEMB
ATOM 6356 H101 POPA 22 -8.934 12.093 3.917 1.00 0.00 MEMB
ATOM 6357 C211 POPA 22 -7.259 13.253 4.785 1.00 -3.44
MEMB
ATOM 6358 H11R POPA 22 -6.510 12.607 4.276 1.00 0.00 MEMB
ATOM 6359 H11S POPA 22 -6.854 13.463 5.801 1.00 0.00 MEMB
ATOM 6360 C212 POPA 22 -7.331 14.601 4.034 1.00 -2.53
MEMB
ATOM 6361 H12R POPA 22 -6.355 15.121 4.157 1.00 0.00 MEMB
ATOM 6362 H12S POPA 22 -8.108 15.238 4.514 1.00 0.00 MEMB
ATOM 6363 C213 POPA 22 -7.642 14.470 2.532 1.00 -1.29
MEMB
ATOM 6364 H13R POPA 22 -8.457 15.169 2.249 1.00 0.00 MEMB
ATOM 6365 H13S POPA 22 -8.008 13.442 2.358 1.00 0.00 MEMB
ATOM 6366 C214 POPA 22 -6.441 14.699 1.603 1.00 -0.54
MEMB
ATOM 6367 H14R POPA 22 -5.628 13.997 1.898 1.00 0.00 MEMB
ATOM 6368 H14S POPA 22 -6.021 15.708 1.737 1.00 0.00 MEMB
ATOM 6369 C215 POPA 22 -6.760 14.476 0.116 1.00 0.38 MEMB
ATOM 6370 H15R POPA 22 -5.982 15.011 -0.495 1.00 0.00 MEMB
ATOM 6371 H15S POPA 22 -7.788 14.771 -0.220 1.00 0.00 MEMB
ATOM 6372 C216 POPA 22 -6.719 13.003 -0.168 1.00 1.38 MEMB
ATOM 6373 H16R POPA 22 -7.194 12.488 0.703 1.00 0.00 MEMB
ATOM 6374 H16S POPA 22 -5.668 12.647 -0.108 1.00 0.00 MEMB
ATOM 6375 C217 POPA 22 -7.629 12.493 -1.353 1.00 2.26 MEMB
ATOM 6376 H17R POPA 22 -7.103 12.927 -2.231 1.00 0.00 MEMB
ATOM 6377 H17S POPA 22 -8.714 12.714 -1.259 1.00 0.00 MEMB
ATOM 6378 C218 POPA 22 -7.509 11.008 -1.453 1.00 3.09 MEMB
ATOM 6379 H18R POPA 22 -7.847 10.511 -0.519 1.00 0.00 MEMB
ATOM 6380 H18S POPA 22 -6.520 10.572 -1.713 1.00 0.00 MEMB
ATOM 6381 H18T POPA 22 -8.258 10.612 -2.171 1.00 0.00 MEMB
ATOM 6382 C33 POPA 22 -16.464 17.039 11.820 1.00-12.04 MEMB
ATOM 6383 H3X POPA 22 -17.560 16.953 11.693 1.00 0.00 MEMB
ATOM 6384 H3Y POPA 22 -16.019 16.368 11.052 1.00 0.00 MEMB
ATOM 6385 C34 POPA 22 -16.090 18.484 11.481 1.00-10.72 MEMB
ATOM 6386 H4X POPA 22 -15.125 18.749 11.972 1.00 0.00 MEMB
ATOM 6387 H4Y POPA 22 -16.873 19.152 11.903 1.00 0.00 MEMB
ATOM 6388 C35 POPA 22 -15.928 18.728 9.974 1.00 -9.86
MEMB
ATOM 6389 H5X POPA 22 -14.961 18.301 9.648 1.00 0.00 MEMB
ATOM 6390 H5Y POPA 22 -15.835 19.806 9.775 1.00 0.00 MEMB
ATOM 6391 C36 POPA 22 -17.057 18.200 9.080 1.00 -8.54
MEMB
ATOM 6392 H6X POPA 22 -18.041 18.549 9.465 1.00 0.00 MEMB
ATOM 6393 H6Y POPA 22 -17.055 17.088 9.085 1.00 0.00 MEMB
ATOM 6394 C37 POPA 22 -16.865 18.708 7.645 1.00 -7.43
MEMB
ATOM 6395 H7X POPA 22 -15.803 18.583 7.354 1.00 0.00 MEMB
ATOM 6396 H7Y POPA 22 -17.018 19.795 7.633 1.00 0.00 MEMB
ATOM 6397 C38 POPA 22 -17.785 18.057 6.608 1.00 -6.21
MEMB
ATOM 6398 H8X POPA 22 -18.835 18.366 6.809 1.00 0.00 MEMB
ATOM 6399 H8Y POPA 22 -17.730 16.950 6.711 1.00 0.00 MEMB
ATOM 6400 C39 POPA 22 -17.404 18.434 5.167 1.00 -5.05
MEMB
ATOM 6401 H9X POPA 22 -16.388 18.042 4.949 1.00 0.00 MEMB
ATOM 6402 H9Y POPA 22 -17.367 19.541 5.069 1.00 0.00 MEMB
ATOM 6403 C310 POPA 22 -18.395 17.870 4.142 1.00 -3.85
MEMB
ATOM 6404 H10X POPA 22 -19.360 18.409 4.265 1.00 0.00 MEMB
ATOM 6405 H10Y POPA 22 -18.570 16.797 4.381 1.00 0.00 MEMB
ATOM 6406 C311 POPA 22 -17.940 17.953 2.674 1.00 -2.66
MEMB
ATOM 6407 H11X POPA 22 -18.798 17.664 2.025 1.00 0.00 MEMB
ATOM 6408 H11Y POPA 22 -17.133 17.205 2.507 1.00 0.00 MEMB
ATOM 6409 C312 POPA 22 -17.419 19.330 2.231 1.00 -1.30
MEMB
ATOM 6410 H12X POPA 22 -16.444 19.506 2.741 1.00 0.00 MEMB
ATOM 6411 H12Y POPA 22 -18.108 20.133 2.554 1.00 0.00 MEMB
ATOM 6412 C313 POPA 22 -17.202 19.416 0.713 1.00 -0.21
MEMB
ATOM 6413 H13X POPA 22 -16.950 18.396 0.342 1.00 0.00 MEMB
ATOM 6414 H13Y POPA 22 -16.321 20.046 0.491 1.00 0.00 MEMB
ATOM 6415 C314 POPA 22 -18.396 19.961 -0.111 1.00 1.01 MEMB
ATOM 6416 H14X POPA 22 -18.686 20.951 0.204 1.00 0.00 MEMB
ATOM 6417 H14Y POPA 22 -19.197 19.234 0.080 1.00 0.00 MEMB
ATOM 6418 C315 POPA 22 -18.024 19.833 -1.597 1.00 1.92 MEMB
ATOM 6419 H15X POPA 22 -17.663 18.829 -1.906 1.00 0.00 MEMB
ATOM 6420 H15Y POPA 22 -17.169 20.513 -1.796 1.00 0.00 MEMB
ATOM 6421 C316 POPA 22 -19.239 20.200 -2.506 1.00 3.28 MEMB
ATOM 6422 H16X POPA 22 -19.011 19.979 -3.570 1.00 0.00 MEMB
ATOM 6423 H16Y POPA 22 -19.546 21.266 -2.437 1.00 0.00 MEMB
ATOM 6424 H16Z POPA 22 -20.104 19.539 -2.286 1.00 0.00 MEMB
thank you very much
best
Albert
On 04/15/2013 08:03 PM, Albert wrote:
Hello Justin and bv08ay:
thanks a lot for kind reply. I count each component by isolating
them one by one:
1. protein generated by pdb2gmx command: 4739 atoms in all
2. ligand: 79 atoms
3. chelostrol: 74x42= 3108 atoms
4. popc: 116x96= 11368 atoms
5. solvent: 10079x3= 30237 atoms
total: 49531
all the above results I double check the no. of coponent and total
line (which represent the atom no.) with gedit, the total atoms is
49621. The toplogy give correct no. of each component, and the total
no. of such component should be 49621 instead of what claimed by
Gromacs " does not match topology (topol.top, 51295) "
It is correct with the topology I defined at the end of topol.top file:
[ molecules ]
; Compound #mols
Protein 1
LIG 1
CHL1 42
POPC 98
SOL 10079
thank you very much
best
Albert
On 04/15/2013 07:45 PM, Justin Lemkul wrote:
Seriously though, the answer to this question is always the same.
You're not counting something right. The solution is something only
you can determine. Applying grep -c is your friend here. You're off
by 1764 atoms, which may be useful information if any of your
molecules are evenly divisible into 1764. Water is, but perhaps other
molecules are, as well, depending on their representation.
-Justin
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