Re: [gmx-users] How to create three different zones to minimize energy of a enzyme?
I suppose it should be mentioned that even with an average desktop computer it should be more than feasible to minimise the whole of your enzyme system. If you want to simulate the system for long periods of time then that is a different question. Tom --On Wednesday, March 19, 2008 08:34:29 +0100 Tsjerk Wassenaar <[EMAIL PROTECTED]> wrote: Hi Lacerda, You should be cautious in the interpretation of your results. Your active site will only be minimized in potential energy in the context of your frozen surface and your restraint internal degrees of freedom. You should be very confident that your surface is about correct and your internal dof are approximately correct in relation to the state of the active site you're interested in. And that's only in terms of energy minimization. If it comes to dynamics, using this approach you would disallow the larger amplitude motions of your system and therefore the coupling with the active site, or actually the meaningful dynamics of the active site. Now, say you want to energy minimize the active site because you put a ligand in. In most cases, the ligand will alter the ensemble. It may very well commute with residues on the surface (allostery?). If you constrain residues which are to respond to the ligand you will add strain to the system which wouldn't be there in the real (unconstrained) thing. You can imagine how this works by placing two magnets together with the equal poles, while constraining them, rather than leaving one to respond to the other. Hope this helps, Tsjerk On Wed, Mar 19, 2008 at 1:51 AM, Mark Abraham <[EMAIL PROTECTED]> wrote: Evanildo Júnior wrote: > Dear gmx-users, > > I would like to minimize the potential energy of the active site of an > enzyme. Because I do not have too much computer power to perform a > full enzyme calculation, I need to create three different zones in > which the calculation will take place. The first one is the outer > boundary of the enzyme that will remain frozen during the calculation. Look for "freeze groups" in the manual. They work with MD and I'm guessing they also work with EM. > The second one is > a transition region between the active site region and the outer > boundary, whose atoms will receive a parabolic potential in order to > move just a little bit. Use position restraints. > The last one is the active site itself which > will be freely minimized. I would like to know how do I implement it > in practice. Does anyone has a Gromacs script for this task? The other > question is how do I freeze only the C-alpha chain? Apply a freeze group only to the C-alpha atoms. You'll need to use make_ndx to make the group and give that index file to grompp as well as the usual stuff. If you're as new to GROMACS as you sound like you might be, you should do some tutorial material and read the first few chapters of the manual thoroughly. Doing the above would not be a good way to get your first exposure to using GROMACS. Mark ___ gmx-users mailing listgmx-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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ gmx-users mailing listgmx-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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- TJ Piggot [EMAIL PROTECTED] University of Bristol, UK. ___ gmx-users mailing listgmx-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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] How to create three different zones to minimize energy of a enzyme?
Hi Lacerda, You should be cautious in the interpretation of your results. Your active site will only be minimized in potential energy in the context of your frozen surface and your restraint internal degrees of freedom. You should be very confident that your surface is about correct and your internal dof are approximately correct in relation to the state of the active site you're interested in. And that's only in terms of energy minimization. If it comes to dynamics, using this approach you would disallow the larger amplitude motions of your system and therefore the coupling with the active site, or actually the meaningful dynamics of the active site. Now, say you want to energy minimize the active site because you put a ligand in. In most cases, the ligand will alter the ensemble. It may very well commute with residues on the surface (allostery?). If you constrain residues which are to respond to the ligand you will add strain to the system which wouldn't be there in the real (unconstrained) thing. You can imagine how this works by placing two magnets together with the equal poles, while constraining them, rather than leaving one to respond to the other. Hope this helps, Tsjerk On Wed, Mar 19, 2008 at 1:51 AM, Mark Abraham <[EMAIL PROTECTED]> wrote: > Evanildo Júnior wrote: > > Dear gmx-users, > > > > I would like to minimize the potential energy of the active site of an > > enzyme. Because I do not have too much computer power to perform a full > > enzyme calculation, I need to create three different zones in which the > > calculation will take place. The first one is the outer boundary of the > > enzyme that will remain frozen during the calculation. > > Look for "freeze groups" in the manual. They work with MD and I'm > guessing they also work with EM. > > > > The second one is > > a transition region between the active site region and the outer > > boundary, whose atoms will receive a parabolic potential in order to > > move just a little bit. > > Use position restraints. > > > > The last one is the active site itself which > > will be freely minimized. I would like to know how do I implement it in > > practice. Does anyone has a Gromacs script for this task? The other > > question is how do I freeze only the C-alpha chain? > > Apply a freeze group only to the C-alpha atoms. You'll need to use > make_ndx to make the group and give that index file to grompp as well as > the usual stuff. > > If you're as new to GROMACS as you sound like you might be, you should > do some tutorial material and read the first few chapters of the manual > thoroughly. Doing the above would not be a good way to get your first > exposure to using GROMACS. > > Mark > ___ > gmx-users mailing listgmx-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 [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ gmx-users mailing listgmx-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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] How to create three different zones to minimize energy of a enzyme?
Evanildo Júnior wrote: Dear gmx-users, I would like to minimize the potential energy of the active site of an enzyme. Because I do not have too much computer power to perform a full enzyme calculation, I need to create three different zones in which the calculation will take place. The first one is the outer boundary of the enzyme that will remain frozen during the calculation. Look for "freeze groups" in the manual. They work with MD and I'm guessing they also work with EM. The second one is a transition region between the active site region and the outer boundary, whose atoms will receive a parabolic potential in order to move just a little bit. Use position restraints. The last one is the active site itself which will be freely minimized. I would like to know how do I implement it in practice. Does anyone has a Gromacs script for this task? The other question is how do I freeze only the C-alpha chain? Apply a freeze group only to the C-alpha atoms. You'll need to use make_ndx to make the group and give that index file to grompp as well as the usual stuff. If you're as new to GROMACS as you sound like you might be, you should do some tutorial material and read the first few chapters of the manual thoroughly. Doing the above would not be a good way to get your first exposure to using GROMACS. Mark ___ gmx-users mailing listgmx-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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] How to create three different zones to minimize energy of a enzyme?
Dear gmx-users, I would like to minimize the potential energy of the active site of an enzyme. Because I do not have too much computer power to perform a full enzyme calculation, I need to create three different zones in which the calculation will take place. The first one is the outer boundary of the enzyme that will remain frozen during the calculation. The second one is a transition region between the active site region and the outer boundary, whose atoms will receive a parabolic potential in order to move just a little bit. The last one is the active site itself which will be freely minimized. I would like to know how do I implement it in practice. Does anyone has a Gromacs script for this task? The other question is how do I freeze only the C-alpha chain? Lacerda Jr. _ Express yourself instantly with MSN Messenger! Download today it's FREE! http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/___ gmx-users mailing listgmx-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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
