[gmx-users] water molecules (interfacial) - IIRC
Dear Mark I have a question as same as atila petrosian, but my system is protein-dna. you said [IIRC g_select has some better documentation available once you run it and ask for help, somewhat like make_ndx]. please explain IIRC more. Is IIRC a program or a list of archives? any help will highly appreciated. -- 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] water molecules (interfacial) - IIRC
On 14/11/2010 7:57 PM, leila karami wrote: Dear Mark I have a question as same as atila petrosian, but my system is protein-dna. you said [IIRC g_select has some better documentation available once you run it and ask for help, somewhat like make_ndx]. please explain IIRC more. Is IIRC a program or a list of archives? IIRC is a standard internet acronym for if I recall correctly In fact, g_select -select help gives access to its online help. Mark -- 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] water molecules (interfacial)
Dear gromacs users I was trying to count waters involved in the interface between Protein_A and Protein_B. I made a selection.dat file as follows: waterO = group SOL and name OW; heavy1 = group Protein_A and group Protein-H; heavy2 = group Protein_B and group Protein-H; inter = waterO and within 0.35 of heavy1 and within 0.35 of heavy2; is my selection.dat file true? I used g_select -f .xtc -s .tpr -n .ndx -os -oc -oi -om -on -sf selection.dat but gromacs: Nothing selected, finishing up. when I used g_select -f .xtc -s .tpr -n .ndx -os -oc -oi -om -on -sf selection.dat -select, what should be put in front of -select to avoid Nothing selected, finishing up? -- 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] water molecules (interfacial)
Dear all my system includes protein, ligand and water. I want to obtain number of water molecules (interfacial) to be within 2.4 A distance from both the protein and the ligand during simulation. also, exact numeration of each water being in interface between protein and ligand. -- 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] water molecules (interfacial)
On 13/11/2010 9:12 PM, atila petrosian wrote: Dear all my system includes protein, ligand and water. I want to obtain number of water molecules (interfacial) to be within 2.4 A distance from both the protein and the ligand during simulation. also, exact numeration of each water being in interface between protein and ligand. Look at the new g_select in GROMACS 4.5.x Mark -- 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] water molecules (interfacial)
Dear Mark and gromacs users thanks for your time and attention. how to make selection.dat file? what should be in that? please clarify this new tool more. how can I obtain what I need (number of water molecules (interfacial) to be within 2.4 A distance from both the protein and the ligand during simulation. also, exact numeration of each water being in interface between protein and ligand)? -- 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] water molecules (interfacial)
atila petrosian wrote: Dear Mark and gromacs users thanks for your time and attention. how to make selection.dat file? what should be in that? please clarify this new tool more. how can I obtain what I need (number of water molecules (interfacial) to be within 2.4 A distance from both the protein and the ligand during simulation. also, exact numeration of each water being in interface between protein and ligand)? I don't know about g_select, but you can do this with g_dist -dist, as well. -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] water molecules (interfacial)
Dear Justin are you sure g_dist -dist give me what I need. if so, how? since, dist.xvg gives distance vs time and lifetime.xvg gives number of contact vs time. while, I want number of water molecules (interfacial) to be within 2.4 A distance from both the protein and the ligand during simulation. also, exact numeration of each water being in interface between protein and ligand. -- 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] water molecules (interfacial)
atila petrosian wrote: Dear Justin are you sure g_dist -dist give me what I need. if so, how? since, dist.xvg gives distance vs time and lifetime.xvg gives number of contact vs time. while, I want number of water molecules (interfacial) to be within 2.4 A distance from both the protein and the ligand during simulation. also, exact numeration of each water being in interface between protein and ligand. If you've only obtained dist.xvg, then you haven't used the -dist flag, which is a separate command line argument. Please see g_dist -h. I think g_select is probably the better tool, but its lack of documentation at the moment makes it very difficult to use. I think g_dist will provide you a suitable alternative. -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] water molecules (interfacial)
Dear Justin I used g_dist -f .xtc -s .tpr -n .ndx -o -lt -dist 1 but program give me only lifetime.xvg. there are no dist.xvg file. why? -- 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] water molecules (interfacial)
On 14/11/2010 12:21 AM, atila petrosian wrote: Dear Mark and gromacs users thanks for your time and attention. how to make selection.dat file? what should be in that? please clarify this new tool more. how can I obtain what I need (number of water molecules (interfacial) to be within 2.4 A distance from both the protein and the ligand during simulation. also, exact numeration of each water being in interface between protein and ligand)? IIRC g_select has some better documentation available once you run it and ask for help, somewhat like make_ndx. Mark -- 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
