Re: [gmx-users] binding_affinity
Hi Justin Before trying for my system I am trying to learn running these simulation with the help of your tutorial. The only change I made is that I applied pull_code for 2nm movement only in order to save time. Thereafter, with trjconv I generated all 200 conf.gro. when I run your perl script it does gives an oitput of summary_distance.dat. It has one column of conf.gro number but no distance. Where I am wrong. Shahid Nayeem On Tue, Apr 19, 2011 at 6:20 PM, Justin A. Lemkul jalem...@vt.edu wrote: Justin A. Lemkul wrote: shahid nayeem wrote: Hi Justin Thanks a lot. What is the purpose of adding 100mM NaCl. Is it mimicking physiological condition. More of a hybrid of physiological and in vitro conditions. Please see the referenced paper for more details. ...and again, please don't necessarily conclude that just because someone did this for a tutorial that you should inherently be doing it for your system. The tutorial is but one example of a workflow, derived from my own specific work. Construct a model that is most appropriate to your purposes. -Justin -- 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/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 -- gmx-users mailing listgmx-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
Re: [gmx-users] binding_affinity
shahid nayeem wrote: Hi Justin Before trying for my system I am trying to learn running these simulation with the help of your tutorial. The only change I made is that I applied pull_code for 2nm movement only in order to save time. Thereafter, with trjconv I generated all 200 conf.gro. when I run your perl script it does gives an oitput of summary_distance.dat. It has one column of conf.gro number but no distance. Where I am wrong. I don't know exactly, but the script runs 500 iterations of each calculation, so you may have 200 lines of content then 300 incomplete lines, unless you've properly modified the script. -Justin Shahid Nayeem On Tue, Apr 19, 2011 at 6:20 PM, Justin A. Lemkul jalem...@vt.edu wrote: Justin A. Lemkul wrote: shahid nayeem wrote: Hi Justin Thanks a lot. What is the purpose of adding 100mM NaCl. Is it mimicking physiological condition. More of a hybrid of physiological and in vitro conditions. Please see the referenced paper for more details. ...and again, please don't necessarily conclude that just because someone did this for a tutorial that you should inherently be doing it for your system. The tutorial is but one example of a workflow, derived from my own specific work. Construct a model that is most appropriate to your purposes. -Justin -- 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 listgmx-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 -- 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 listgmx-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
Re: [gmx-users] binding_affinity
Hi Justin I went through your tutorial of umbrella sampling. Please clarify that while generating configuration one requires index.ndx of certain residue. These residue are from the restrained chain or from the chain on which pulling force is to be applied in order to separate the chain. why two groups are created. Does index.ndx should contain all residue from the chain which has to move or few are sufficient. Shahid Nayeem On Thu, Apr 14, 2011 at 6:34 PM, Justin A. Lemkul jalem...@vt.edu wrote: shahid nayeem wrote: Dear All I have some protein complex pdb after docking two monomers. The scoring of these docked structure are not true representative of binding affinity. I want calculate the binding affinity affinity of these docked pdb. Can anyone suggest me, how should I proceed. Shahid Nayeem Calculating a PMF is a common approach. http://www.gromacs.org/Documentation/How-tos/Potential_of_Mean_Force -Justin -- 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/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 -- gmx-users mailing listgmx-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
Re: [gmx-users] binding_affinity
shahid nayeem wrote: Hi Justin I went through your tutorial of umbrella sampling. Please clarify that while generating configuration one requires index.ndx of certain residue. These residue are from the restrained chain or from the chain on which pulling force is to be applied in order to separate the chain. why two groups are created. Does index.ndx should contain all residue from the chain which has to move or few are sufficient. Do what is appropriate for your system. The reasons for the restraints I used are described in my paper that I link from the tutorial. I certainly hope you've read it to understand the methodology. Thus you do not necessarily have to apply the exact methodology to get a sensible result. You need two groups - a reference group and a group to which the pulling force is applied. Maybe your reference group (whatever it is) needs to be restrained to avoid structural deformation, maybe it doesn't. Whether or not an index file is necessary also depends on how you set up the reference and pulled groups. If they are default groups, then you don't need an index file, but if they are some subset of existing groups, then yes, you need a custom index file, just like any other Gromacs operation. -Justin Shahid Nayeem On Thu, Apr 14, 2011 at 6:34 PM, Justin A. Lemkul jalem...@vt.edu wrote: shahid nayeem wrote: Dear All I have some protein complex pdb after docking two monomers. The scoring of these docked structure are not true representative of binding affinity. I want calculate the binding affinity affinity of these docked pdb. Can anyone suggest me, how should I proceed. Shahid Nayeem Calculating a PMF is a common approach. http://www.gromacs.org/Documentation/How-tos/Potential_of_Mean_Force -Justin -- 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 listgmx-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 -- 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 listgmx-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
Re: [gmx-users] binding_affinity
Hi Justin Thanks a lot. What is the purpose of adding 100mM NaCl. Is it mimicking physiological condition. Shahid Nayeem On Tue, Apr 19, 2011 at 5:47 PM, Justin A. Lemkul jalem...@vt.edu wrote: shahid nayeem wrote: Hi Justin I went through your tutorial of umbrella sampling. Please clarify that while generating configuration one requires index.ndx of certain residue. These residue are from the restrained chain or from the chain on which pulling force is to be applied in order to separate the chain. why two groups are created. Does index.ndx should contain all residue from the chain which has to move or few are sufficient. Do what is appropriate for your system. The reasons for the restraints I used are described in my paper that I link from the tutorial. I certainly hope you've read it to understand the methodology. Thus you do not necessarily have to apply the exact methodology to get a sensible result. You need two groups - a reference group and a group to which the pulling force is applied. Maybe your reference group (whatever it is) needs to be restrained to avoid structural deformation, maybe it doesn't. Whether or not an index file is necessary also depends on how you set up the reference and pulled groups. If they are default groups, then you don't need an index file, but if they are some subset of existing groups, then yes, you need a custom index file, just like any other Gromacs operation. -Justin Shahid Nayeem On Thu, Apr 14, 2011 at 6:34 PM, Justin A. Lemkul jalem...@vt.edu wrote: shahid nayeem wrote: Dear All I have some protein complex pdb after docking two monomers. The scoring of these docked structure are not true representative of binding affinity. I want calculate the binding affinity affinity of these docked pdb. Can anyone suggest me, how should I proceed. Shahid Nayeem Calculating a PMF is a common approach. http://www.gromacs.org/Documentation/How-tos/Potential_of_Mean_Force -Justin -- 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/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 -- 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/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 -- gmx-users mailing listgmx-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
Re: [gmx-users] binding_affinity
shahid nayeem wrote: Hi Justin Thanks a lot. What is the purpose of adding 100mM NaCl. Is it mimicking physiological condition. More of a hybrid of physiological and in vitro conditions. Please see the referenced paper for more details. -Justin Shahid Nayeem On Tue, Apr 19, 2011 at 5:47 PM, Justin A. Lemkul jalem...@vt.edu wrote: shahid nayeem wrote: Hi Justin I went through your tutorial of umbrella sampling. Please clarify that while generating configuration one requires index.ndx of certain residue. These residue are from the restrained chain or from the chain on which pulling force is to be applied in order to separate the chain. why two groups are created. Does index.ndx should contain all residue from the chain which has to move or few are sufficient. Do what is appropriate for your system. The reasons for the restraints I used are described in my paper that I link from the tutorial. I certainly hope you've read it to understand the methodology. Thus you do not necessarily have to apply the exact methodology to get a sensible result. You need two groups - a reference group and a group to which the pulling force is applied. Maybe your reference group (whatever it is) needs to be restrained to avoid structural deformation, maybe it doesn't. Whether or not an index file is necessary also depends on how you set up the reference and pulled groups. If they are default groups, then you don't need an index file, but if they are some subset of existing groups, then yes, you need a custom index file, just like any other Gromacs operation. -Justin Shahid Nayeem On Thu, Apr 14, 2011 at 6:34 PM, Justin A. Lemkul jalem...@vt.edu wrote: shahid nayeem wrote: Dear All I have some protein complex pdb after docking two monomers. The scoring of these docked structure are not true representative of binding affinity. I want calculate the binding affinity affinity of these docked pdb. Can anyone suggest me, how should I proceed. Shahid Nayeem Calculating a PMF is a common approach. http://www.gromacs.org/Documentation/How-tos/Potential_of_Mean_Force -Justin -- 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 listgmx-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 -- 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 listgmx-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 -- 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 listgmx-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
Re: [gmx-users] binding_affinity
Justin A. Lemkul wrote: shahid nayeem wrote: Hi Justin Thanks a lot. What is the purpose of adding 100mM NaCl. Is it mimicking physiological condition. More of a hybrid of physiological and in vitro conditions. Please see the referenced paper for more details. ...and again, please don't necessarily conclude that just because someone did this for a tutorial that you should inherently be doing it for your system. The tutorial is but one example of a workflow, derived from my own specific work. Construct a model that is most appropriate to your purposes. -Justin -- 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 listgmx-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
[gmx-users] binding_affinity
Dear All I have some protein complex pdb after docking two monomers. The scoring of these docked structure are not true representative of binding affinity. I want calculate the binding affinity affinity of these docked pdb. Can anyone suggest me, how should I proceed. Shahid Nayeem -- gmx-users mailing listgmx-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
Re: [gmx-users] binding_affinity
shahid nayeem wrote: Dear All I have some protein complex pdb after docking two monomers. The scoring of these docked structure are not true representative of binding affinity. I want calculate the binding affinity affinity of these docked pdb. Can anyone suggest me, how should I proceed. Shahid Nayeem Calculating a PMF is a common approach. http://www.gromacs.org/Documentation/How-tos/Potential_of_Mean_Force -Justin -- 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 listgmx-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
