Re:[gmx-users] Lysozyme in Water at different pH and Ionic strength
It is impossible. But you can add proton to the acidic amino acid. At 2013-11-01 20:36:41,Mass masstransfer_2...@yahoo.com wrote: Dear Gromacs users, Just was wondering if it is possible to protein solution let say Lysozyme in Water example of Justin tutorial at different pH and ionic strengths, if so how? Thanks -- 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 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] Lysozyme in Water at different pH and Ionic strength
On 11/1/13 8:39 AM, xiao wrote: It is impossible. But you can add proton to the acidic amino acid. It's certainly not impossible. There are constant-pH methods that exist; the list archive contains many posts on this topic, and more information can be found at: http://www.gromacs.org/Documentation/How-tos/Constant_pH_Simulation Whether or not you can easily accomplish such simulations in Gromacs is another matter. Standard MD does not allow for dynamic protonation states, so the closest you can get without running more advanced MD is to use fixed protonation states, assigned by pdb2gmx, that are indicative of the most prevalent state of the residues at a given pH value. Changing ionic strength is trivial; that's what genion -conc is for. -Justin At 2013-11-01 20:36:41,Mass masstransfer_2...@yahoo.com wrote: Dear Gromacs users, Just was wondering if it is possible to protein solution let say Lysozyme in Water example of Justin tutorial at different pH and ionic strengths, if so how? Thanks -- 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. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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] Lysozyme in Water at different pH and Ionic strength
Following up on Justin's reply I just want to add that, not only is it possible, as it has been done before. For instance: http://www.ncbi.nlm.nih.gov/pubmed/18214978 http://www.ncbi.nlm.nih.gov/pubmed/22072522 Luís Filipe ITQB-UNL, Portugal 2013/11/1 Justin Lemkul jalem...@vt.edu On 11/1/13 8:39 AM, xiao wrote: It is impossible. But you can add proton to the acidic amino acid. It's certainly not impossible. There are constant-pH methods that exist; the list archive contains many posts on this topic, and more information can be found at: http://www.gromacs.org/**Documentation/How-tos/**Constant_pH_Simulationhttp://www.gromacs.org/Documentation/How-tos/Constant_pH_Simulation Whether or not you can easily accomplish such simulations in Gromacs is another matter. Standard MD does not allow for dynamic protonation states, so the closest you can get without running more advanced MD is to use fixed protonation states, assigned by pdb2gmx, that are indicative of the most prevalent state of the residues at a given pH value. Changing ionic strength is trivial; that's what genion -conc is for. -Justin At 2013-11-01 20:36:41,Mass masstransfer_2...@yahoo.com wrote: Dear Gromacs users, Just was wondering if it is possible to protein solution let say Lysozyme in Water example of Justin tutorial at different pH and ionic strengths, if so how? Thanks -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://www.gromacs.org/Support/Mailing_Lists -- ==** Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 ==** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://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] Lysozyme in Water at different pH and Ionic strength
I notice that both papers mention modifications to GROMACS and cite the following: http://www.ncbi.nlm.nih.gov/pubmed/16471903 Following up on Justin's reply I just want to add that, not only is it possible, as it has been done before. For instance: http://www.ncbi.nlm.nih.gov/pubmed/18214978 http://www.ncbi.nlm.nih.gov/pubmed/22072522 Luís Filipe ITQB-UNL, Portugal 2013/11/1 Justin Lemkul jalem...@vt.edu On 11/1/13 8:39 AM, xiao wrote: It is impossible. But you can add proton to the acidic amino acid. It's certainly not impossible. There are constant-pH methods that exist; the list archive contains many posts on this topic, and more information can be found at: http://www.gromacs.org/**Documentation/How-tos/**Constant_pH_Simulationhttp://www.gromacs.org/Documentation/How-tos/Constant_pH_Simulation Whether or not you can easily accomplish such simulations in Gromacs is another matter. Standard MD does not allow for dynamic protonation states, so the closest you can get without running more advanced MD is to use fixed protonation states, assigned by pdb2gmx, that are indicative of the most prevalent state of the residues at a given pH value. Changing ionic strength is trivial; that's what genion -conc is for. -Justin At 2013-11-01 20:36:41,Mass masstransfer_2...@yahoo.com wrote: Dear Gromacs users, Just was wondering if it is possible to protein solution let say Lysozyme in Water example of Justin tutorial at different pH and ionic strengths, if so how? Thanks -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://www.gromacs.org/Support/Mailing_Lists -- ==** Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 ==** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://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 -- 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
