[gmx-users] why no. of atoms doesn't match?
Albert
mailmd2011 at gmail.com
Mon Apr 15 20:29:52 CEST 2013
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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