Thanks a lot Justin..... On Wed, Aug 29, 2012 at 11:57 PM, Justin Lemkul <jalem...@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 > > ======================================== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the www > interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
-- 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 -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
