[gmx-users] extra Oxygen ....upon modification of middle residue

Justin Lemkul jalemkul at vt.edu
Wed Aug 29 20:27:38 CEST 2012



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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