[gmx-users] extra Oxygen ....upon modification of middle residue
tarak karmakar
tarak20489 at gmail.com
Thu Aug 30 06:24:16 CEST 2012
Thanks a lot Justin.....
On Wed, Aug 29, 2012 at 11:57 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> On 8/29/12 2:19 PM, tarak karmakar wrote:
>>
>> 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 ?
>
>
> Likely you forgot step #5 here:
>
> http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field#Adding_a_new_residue
>
> If pdb2gmx detects a change in the type of residue (i.e. HIP being protein,
> TYU being unknown) it creates a terminus and thus you see a carboxylate
> instead of a carbonyl in the amide.
>
> -Justin
>
> --
> ========================================
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
> --
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--
Tarak Karmakar
Molecular Simulation Lab.
Chemistry and Physics of Materials Unit
Jawaharlal Nehru Centre for Advanced Scientific Research
Jakkur P. O.
Bangalore - 560 064
Karnataka, INDIA
Ph. (lab) : +91-80-22082809
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