[gmx-users] extra Oxygen ....upon modification of middle residue
tarak karmakar
tarak20489 at gmail.com
Wed Aug 29 20:19:09 CEST 2012
Dear All,
In my protein pdb file I am changing the protonation state of residue
and giving some other name to it . Now after creating the .gro file I
see that the residue present before the modified one has been
considered as the C-terminal and it is adding one extra oxygen atom to
it. I am giving parts of the pdb and .gro file below. Please have a
look and suggest me something to avoid this issue.
"pdb" file
ATOM 5287 N HIP A 339 12.427 -2.647 26.276 N
ATOM 5288 H HIP A 339 12.262 -2.799 25.291 H
ATOM 5289 CA HIP A 339 13.294 -3.555 27.014 C
ATOM 5290 HA HIP A 339 13.913 -2.977 27.668 H
ATOM 5291 C HIP A 339 14.188 -4.357 26.088 C
ATOM 5292 O HIP A 339 13.886 -4.534 24.907 O
ATOM 5293 CB HIP A 339 12.454 -4.516 27.862 C
ATOM 5294 HB1 HIP A 339 11.771 -3.937 28.454 H
ATOM 5295 HB2 HIP A 339 13.114 -5.062 28.509 H
ATOM 5296 CG HIP A 339 11.664 -5.499 27.054 C
ATOM 5297 ND1 HIP A 339 12.094 -6.787 26.820 N
ATOM 5298 CD2 HIP A 339 10.483 -5.373 26.403 C
ATOM 5299 HD2 HIP A 339 9.858 -4.488 26.370 H
ATOM 5300 CE1 HIP A 339 11.213 -7.413 26.060 C
ATOM 5301 HE1 HIP A 339 11.287 -8.438 25.715 H
ATOM 5302 NE2 HIP A 339 10.226 -6.577 25.792 N
ATOM 5303 HE2 HIP A 339 9.414 -6.788 25.229 H
ATOM 5304 N TYU A 340 15.300 -4.830 26.639 N
ATOM 5305 H TYU A 340 15.501 -4.607 27.603 H
ATOM 5306 CA TYU A 340 16.236 -5.658 25.899 C
ATOM 5307 HA TYU A 340 16.130 -5.490 24.848 H
ATOM 5308 C TYU A 340 15.887 -7.100 26.242 C
ATOM 5309 O TYU A 340 15.583 -7.417 27.392 O
ATOM 5310 CB TYU A 340 17.673 -5.385 26.338 C
ATOM 5311 HB1 TYU A 340 17.736 -5.511 27.402 H
ATOM 5312 HB2 TYU A 340 17.922 -4.373 26.083 H
ATOM 5313 CG TYU A 340 18.674 -6.308 25.683 C
ATOM 5314 CD1 TYU A 340 19.195 -6.021 24.422 C
ATOM 5315 HD1 TYU A 340 18.903 -5.105 23.921 H
ATOM 5316 CD2 TYU A 340 19.068 -7.493 26.304 C
ATOM 5317 HD2 TYU A 340 18.678 -7.735 27.286 H
ATOM 5318 CE1 TYU A 340 20.086 -6.892 23.794 C
ATOM 5319 HE1 TYU A 340 20.484 -6.652 22.814 H
ATOM 5320 CE2 TYU A 340 19.956 -8.372 25.683 C
ATOM 5321 HE2 TYU A 340 20.250 -9.290 26.178 H
ATOM 5322 CZ TYU A 340 20.459 -8.063 24.429 C
ATOM 5323 OH TYU A 340 21.332 -8.928 23.807 O
ATOM 5325 N ALA A 341 15.925 -7.977 25.249 N
ATOM 5326 H ALA A 341 16.165 -7.672 24.317 H
ATOM 5327 CA ALA A 341 15.623 -9.376 25.497 C
ATOM 5328 HA ALA A 341 15.992 -9.645 26.465 H
ATOM 5329 C ALA A 341 16.301 -10.235 24.456 C
ATOM 5330 O ALA A 341 16.372 -9.864 23.286 O
ATOM 5331 CB ALA A 341 14.118 -9.606 25.459 C
ATOM 5332 HB1 ALA A 341 13.633 -8.991 26.233 H
ATOM 5333 HB2 ALA A 341 13.729 -9.324 24.468 H
ATOM 5334 HB3 ALA A 341 13.904 -10.669 25.648 H
note that I have deprotonated 'TYR' side chain and gave new name as
"TYU" but see the .gro file ...............in residue 'HIP' one extra
Oxygen came and has been considered as the C-terminal of the protein
339HIP N 5291 1.243 -0.265 2.628
339HIP H 5292 1.226 -0.280 2.529
339HIP CA 5293 1.329 -0.356 2.701
339HIP HA 5294 1.391 -0.298 2.767
339HIP CB 5295 1.245 -0.452 2.786
339HIP HB1 5296 1.177 -0.394 2.845
339HIP HB2 5297 1.311 -0.506 2.851
339HIP CG 5298 1.166 -0.550 2.705
339HIP ND1 5299 1.209 -0.679 2.682
339HIP HD1 5300 1.294 -0.719 2.717
339HIP CE1 5301 1.121 -0.741 2.606
339HIP HE1 5302 1.129 -0.844 2.572
339HIP NE2 5303 1.023 -0.658 2.579
339HIP HE2 5304 0.941 -0.679 2.523
339HIP CD2 5305 1.048 -0.537 2.640
339HIP HD2 5306 0.986 -0.449 2.637
339HIP C 5307 1.419 -0.436 2.609
339HIP OC1 5308 1.504 -0.475 2.644
339HIP OC2 5309 1.389 -0.453 2.491
340TYU N 5310 1.530 -0.483 2.664
340TYU H 5311 1.550 -0.461 2.760
340TYU CA 5312 1.624 -0.566 2.590
340TYU HA 5313 1.613 -0.549 2.485
340TYU CB 5314 1.767 -0.539 2.634
340TYU HB1 5315 1.774 -0.551 2.740
340TYU HB2 5316 1.792 -0.437 2.608
340TYU CG 5317 1.867 -0.631 2.568
340TYU CD1 5318 1.919 -0.602 2.442
340TYU HD1 5319 1.890 -0.511 2.392
340TYU CE1 5320 2.009 -0.689 2.379
340TYU HE1 5321 2.048 -0.665 2.281
340TYU CZ 5322 2.046 -0.806 2.443
340TYU OH 5323 2.133 -0.893 2.381
340TYU CE2 5324 1.996 -0.837 2.568
340TYU HE2 5325 2.025 -0.929 2.618
340TYU CD2 5326 1.907 -0.749 2.630
340TYU HD2 5327 1.868 -0.774 2.729
340TYU C 5328 1.589 -0.710 2.624
340TYU O 5329 1.558 -0.742 2.739
341ALA N 5330 1.592 -0.798 2.525
341ALA H 5331 1.617 -0.767 2.432
341ALA CA 5332 1.562 -0.938 2.550
341ALA HA 5333 1.599 -0.965 2.647
341ALA CB 5334 1.412 -0.961 2.546
341ALA HB1 5335 1.363 -0.899 2.623
341ALA HB2 5336 1.373 -0.932 2.447
341ALA HB3 5337 1.390 -1.067 2.565
341ALA C 5338 1.630 -1.023 2.446
341ALA O 5339 1.637 -0.986 2.329
Please tell me something why it's happening so ?
Thanks,
Tarak
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