Do single-point MM/PBSA calculations. That's an energy value. But they may or may not be accurate. "Energy values" as you put them are not simple and you may need to run a simulation in order to obtain a proper ensemble. Such a simulation is not for "refining the structure", it's to obtain an ensemble. Then MM/PBSA or MM/GBSA may yield more accurate values of energy when you use the ensemble of structures to perform these calculations.
Quoting abdullah ahmed <abdullah_renk_ah...@hotmail.com>: > > The charged residues are on the inside of the structure, and so are not > affected by the solvent. There are also no other charged residues in the > structure. Furthermore, the structure is quite small 22 (residues). So I am > still tempted to say that the coloumbic energy of the system should be > affected by these charges. > > Regarding MD, the structure I am using is already in an optimal position. I > am not particularly interested in refining the structure. All I really need > is the energy value. > > > Date: Tue, 4 May 2010 08:53:48 -0400 > > From: jalem...@vt.edu > > To: gmx-users@gromacs.org > > Subject: Re: [gmx-users] electro-static potential energy after > minimization > > > > > > > > abdullah ahmed wrote: > > > Thank you for your reply, > > > > > > However, I can not use MD. > > > I would simply like to ask whether I am correct in assuming that the > > > minimized energies of the two structures should be very different. > > > > > > > What exactly are you measuring? The Coulombic energy of the system? If > so, > > that term is going to be largely controlled by the solvent and thus you > will see > > little, if any, difference at all between the two systems. If you're > measuring > > the Coulombic energy between two residues, yes, you should see a clear > difference. > > > > I don't understand your argument against MD. To me, restrained > minimization > > doesn't tell you much at all. But maybe I don't fully grasp your > intentions for > > these calculations. > > > > -Justin > > > > > > Date: Tue, 4 May 2010 08:41:15 -0400 > > > > From: jalem...@vt.edu > > > > To: gmx-users@gromacs.org > > > > Subject: Re: [gmx-users] electro-static potential energy after > > > minimization > > > > > > > > > > > > > > > > abdullah ahmed wrote: > > > > > Hello everyone, > > > > > > > > > > I have two protein structures, and the insides of both are not > exposed > > > > > to water. > > > > > One structure contains two oppositely charges residues (GLU and > LYS) > > > > > facing each other. The second structure contains a GLU residue > only. > > > > > Upon minimization I had expected the coloumb energies of the first > > > > > structure to be lower than that of the second. However, this was > > > not the > > > > > case, they are both very similar. > > > > > Does anyone have an idea as to why this has happened? > > > > > (The only explaination I can come up with is that perhaps the > > > effect is > > > > > so small that it can not be seen) > > > > > > > > > > > > > We discussed this at length yesterday. By doing a simple energy > > > minimization > > > > (in which, if I recall, you are applying position restraints), you > > > stand to > > > > prove very little. By doing MD and obtaining an ensemble of energies, > > > > you stand > > > > a better chance of calculating a relevant energy. > > > > > > > > > I was not sure if providing PDB and .mdp files would be helpful, but > I > > > > > can send then in my next mail if neccesary. > > > > > > > > > > > > > The .pdb file is unnecessary. Only post the .mdp file if it has > > > changed since > > > > the one you posted yesterday. > > > > > > > > -Justin > > > > > > > > > Thank you in advance! > > > > > Abdullah Ahmed > > > > > > > > > > > > > ------------------------------------------------------------------------ > > > > > Your E-mail and More On-the-Go. Get Windows Live Hotmail Free. Sign > up > > > > > now. <https://signup.live.com/signup.aspx?id=60969> > > > > > > > > > > > > > -- > > > > ======================================== > > > > > > > > Justin A. Lemkul > > > > Ph.D. Candidate > > > > ICTAS Doctoral Scholar > > > > MILES-IGERT Trainee > > > > 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/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 > > > > > > ------------------------------------------------------------------------ > > > Hotmail: Trusted email with Microsofts powerful SPAM protection. Sign > > > up now. <https://signup.live.com/signup.aspx?id=60969> > > > > > > > -- > > ======================================== > > > > Justin A. Lemkul > > Ph.D. Candidate > > ICTAS Doctoral Scholar > > MILES-IGERT Trainee > > 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/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 > > Hotmail: Free, trusted and rich email service. Get it now. > _________________________________________________________________ > Hotmail: Free, trusted and rich email service. > https://signup.live.com/signup.aspx?id=60969 -- Jared James Thompson Department of Medicinal Chemistry and Molecular Pharmacology Laboratory for Computational Drug Design and Biology RHPH 504C Heine Pharmacy Building 575 Stadium Mall Drive West Lafayette, IN 47907-2091 -- 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/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
