Dear Gerrit, Thanks for your kind reply! I just forget covalent bonds!
Best regards, Seungpyo Hong On Fri, Mar 6, 2009 at 8:05 PM, Gerrit Groenhof <ggro...@gwdg.de> wrote: > Coulomb 1-4 is only beteen the atoms that are 3 bonds away from each other. > The bonds prevent these atoms to get apart too far, so 1-4 won't destabilize > the overall structure. The SR part is negative, thus keeping your protein > together. > > Gerrit > > > >> Message: 3 >> Date: Fri, 6 Mar 2009 19:43:19 +0900 >> From: Seungpyo Hong <sp1...@gmail.com> >> Subject: [gmx-users] Positive energy for Coulumb term. Does this mean >> Coulumb interaction destabilizes protein? >> To: gmx-users@gromacs.org >> Message-ID: >> <bd5475eb0903060243q7a553766r70664758fa47f...@mail.gmail.com> >> Content-Type: text/plain; charset="iso-8859-1" >> >> Dear GMX-Users, >> >> As I analyze energy terms of proteins, I found something looks weird. >> I thought that fullly folded proteins are stabilized by Coulomb >> interaction >> (such as hydrogen bonds). >> However, what I found embarasses me. >> >> The Coulomb interaction seems to destabilize the protein structure as its >> energy is positive. >> >> Coul-SR + Coul-14 = 32 > 0 >> Coul-SR + Coul-14 + Coul-SR(Protein-Non-Protein) = 18 > 0 >> >> >> Energy Average RMSD Fluct. Drift >> Tot-Drift >> >> ------------------------------------------------------------------------------- >> Coul-SR:Protein-Protein -11.6253 365.244 357.507 -0.735925 >> -259.047 >> LJ-SR:Protein-Protein -6.51389 204.554 203.627 0.191426 >> 67.3824 >> Coul-14:Protein-Protein 38.5848 1212.26 1196.75 1.90253 >> 669.696 >> LJ-14:Protein-Protein 3.58465 112.688 112.645 -0.0303438 >> -10.6811 >> Coul-SR:Protein-Non-Protein -14.1247 443.927 437.195 -0.75795 >> -266.8 >> LJ-SR:Protein-Non-Protein -1.51471 47.6924 46.2568 -0.11429 >> -40.2302 >> >> >> I thought of the total charge of the protein; but it is only +2. >> And, the structure is quite stable through the simulation. (RMSD: 0.17) >> >> I am quite confusing about the effect of Coulumb interaction on the >> stability of the protein. >> I feel like I am missing very important concept about the stability of >> protein or the energy term used here. >> Can anyone help me to understand the effect of Coulumb interaction in the >> stability of the protein? >> >> Any opinion or comment would be great help for me. >> >> Thank you very much! >> >> Sincerely, >> Seungpyo Hong >> >> >> > > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php > -- -------------------------------------------------- 'God used beautiful mathematics in creating the world.' -Paul Dirac 'At the same time, he allowed interaction among objects.' -Seungpyo Hong Seungpyo Hong Master student at PBIL(Protein BioInformatics Lab.) in KAIST, Daejeon Korea Tel. (82)-18-372-2468 spho...@kaist.ac.kr sp1...@gmail.com
_______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php