Dear Gerrit, <br><br>Thanks for your kind reply!<br>I just forget covalent bonds!<br><br>Best regards, <br>Seungpyo Hong<br><br><div class="gmail_quote">On Fri, Mar 6, 2009 at 8:05 PM, Gerrit Groenhof <span dir="ltr"><<a href="mailto:ggroenh@gwdg.de">ggroenh@gwdg.de</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">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.<br>
<br>
Gerrit<br>
<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<br>
Message: 3<br>
Date: Fri, 6 Mar 2009 19:43:19 +0900<br>
From: Seungpyo Hong <<a href="mailto:sp1020@gmail.com" target="_blank">sp1020@gmail.com</a>><br>
Subject: [gmx-users] Positive energy for Coulumb term. Does this mean<br>
Coulumb interaction destabilizes protein?<br>
To: <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
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<<a href="mailto:bd5475eb0903060243q7a553766r70664758fa47f88c@mail.gmail.com" target="_blank">bd5475eb0903060243q7a553766r70664758fa47f88c@mail.gmail.com</a>><br>
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<br>
Dear GMX-Users,<br>
<br>
As I analyze energy terms of proteins, I found something looks weird.<br>
I thought that fullly folded proteins are stabilized by Coulomb interaction<br>
(such as hydrogen bonds).<br>
However, what I found embarasses me.<br>
<br>
The Coulomb interaction seems to destabilize the protein structure as its<br>
energy is positive.<br>
<br>
Coul-SR + Coul-14 = 32 > 0<br>
Coul-SR + Coul-14 + Coul-SR(Protein-Non-Protein) = 18 > 0<br>
<br>
<br>
Energy Average RMSD Fluct. Drift<br>
Tot-Drift<br>
-------------------------------------------------------------------------------<br>
Coul-SR:Protein-Protein -11.6253 365.244 357.507 -0.735925<br>
-259.047<br>
LJ-SR:Protein-Protein -6.51389 204.554 203.627 0.191426<br>
67.3824<br>
Coul-14:Protein-Protein 38.5848 1212.26 1196.75 1.90253<br>
669.696<br>
LJ-14:Protein-Protein 3.58465 112.688 112.645 -0.0303438<br>
-10.6811<br>
Coul-SR:Protein-Non-Protein -14.1247 443.927 437.195 -0.75795<br>
-266.8<br>
LJ-SR:Protein-Non-Protein -1.51471 47.6924 46.2568 -0.11429<br>
-40.2302<br>
<br>
<br>
I thought of the total charge of the protein; but it is only +2.<br>
And, the structure is quite stable through the simulation. (RMSD: 0.17)<br>
<br>
I am quite confusing about the effect of Coulumb interaction on the<br>
stability of the protein.<br>
I feel like I am missing very important concept about the stability of<br>
protein or the energy term used here.<br>
Can anyone help me to understand the effect of Coulumb interaction in the<br>
stability of the protein?<br>
<br>
Any opinion or comment would be great help for me.<br>
<br>
Thank you very much!<br>
<br>
Sincerely,<br>
Seungpyo Hong<br>
<br>
<br>
</blockquote>
<br>
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</blockquote></div><br><br clear="all"><br>-- <br>--------------------------------------------------<br>'God used beautiful mathematics in creating the world.'<br>-Paul Dirac <br>'At the same time, he allowed interaction among objects.'<br>
-Seungpyo Hong <br><br>Seungpyo Hong <br>Master student at PBIL(Protein BioInformatics Lab.) in KAIST, Daejeon Korea<br>Tel. (82)-18-372-2468<br><a href="mailto:sphong_@kaist.ac.kr">sphong_@kaist.ac.kr</a><br><a href="mailto:sp1020@gmail.com">sp1020@gmail.com</a><br>