[gmx-users] Fw:some waters in active site of receptor
Dear, there are three waters in active site of receptor,mediating the binding of ligand with target protein. i want to study the three waters how to affect the binding of ligand with target protein and the contribution to the stability of the system. In order to avoid the three waters exchange with the solvent waters, can i do the ligand-receptor in the implicit solvent. i will prepare two diffrent recepor mode. The one is not water in active site and the other retain waters in the active site. my ideal is good or not? Forwarding messages From: aixintiankong Date: 2013-02-16 23:54:51 To: gmx-users@gromacs.org Subject: some waters in active site of receptor Dear, there are three waters in active site of receptor, mediating the binding of ligand with target protein. i want to study the three waters how to affect the binding of ligand with target protein and the contribution to the stability of the system. In order to study the role of the waters, i want to compare some diffrent system models. The first model have all a waters in active site ,the second model have two waters and the third have one water , the fourth have none water in acitve site. however, i don't know how to construct simulation models of those. when i use the genbox program to add solvent to my system, i find there are many other waters being added to the active site and i think the waters which are added by genbox program maybe replace the initial three waters and then i can't study the waters in active site. please hlpe me and then tell me how to do it Thank you very much! -- 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] Fw:some waters in active site of receptor
On 2/16/13 8:37 PM, aixintiankong wrote: Forwarding messages From: aixintiankong Date: 2013-02-16 23:54:51 To: gmx-users@gromacs.org Subject: some waters in active site of receptor Dear, there are three waters in active site of receptor, mediating the binding of ligand with target protein. i want to study the three waters how to affect the binding of ligand with target protein and the contribution to the stability of the system. In order to study the role of the waters, i want to compare some diffrent system models. The first model have all a waters in active site ,the second model have two waters and the third have one water , the fourth have none water in acitve site. however, i don't know how to construct simulation models of those. when i use the genbox program to add solvent to my system, i find there are many other waters being added to the active site and i think the waters which are added by genbox program maybe replace the initial three waters and then i can't study the waters in active site. please hlpe me and then tell me how to do it genbox does not replace water molecules, it only adds more. Your original three waters should always be the first three listed after the end of the protein/ligand coordinates. You could always temporarily rename them (from SOL to HOH, for instance), run the solvation, and verify this yourself. Running genion is the trickier part because the waters of interest stand a small chance of being randomly replaced, though the same renaming strategy could apply. As for the intent of the study, that's harder to say, because if there's enough room for more water to flood in, what makes those waters so special? They could easily be exchanged for others that might diffuse in. I'm afraid I don't have any brilliant insights as far as experimental design goes. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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] Fw:some waters in active site of receptor
Forwarding messages From: aixintiankong Date: 2013-02-16 23:54:51 To: gmx-users@gromacs.org Subject: some waters in active site of receptor Dear, there are three waters in active site of receptor, mediating the binding of ligand with target protein. i want to study the three waters how to affect the binding of ligand with target protein and the contribution to the stability of the system. In order to study the role of the waters, i want to compare some diffrent system models. The first model have all a waters in active site ,the second model have two waters and the third have one water , the fourth have none water in acitve site. however, i don't know how to construct simulation models of those. when i use the genbox program to add solvent to my system, i find there are many other waters being added to the active site and i think the waters which are added by genbox program maybe replace the initial three waters and then i can't study the waters in active site. please hlpe me and then tell me how to do it Thank you very much! -- 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
