Re: [gmx-users] several questions about g_hbond -contact
Anna Marabotti wrote: Dear users, I'm using g_hbond with option -contact in order to find the contacts between my protein and a series of ligands, in a radius of 0.5 nm. I made several calculations but I'm quite uncertain about the results, therefore I'm asking you some questions. The command I used is: g_hbond -f my_prot.xtc -s my_prot.tpr -n index.ndx -g logfile.log -num contact_num.xvg -hbn contact.ndx -hbm contact.xpm -contact (for options -r and -r2 see below). Here my questions: 1) I have to indicate two groups when prompted. If I select first "1" (protein) and then "15" (ligand), the program does not find contacts (it calculates, but says "No contacts found"). On the contrary, if I first select "15" and then "1", the program finds contacts. Why? I'm expecting that if an atom of the protein contacts an atom of the ligand, it is a reversible thing, especially because this is not a H-bond in which the different order D-A could affect the results. To proceed with my test, I always selected first "15" and then "1". 2) If I fix only -r 0.5, the program starts calculating. It finds a number of "donor" and "acceptor" atoms and starts doing a grid search on a 18x18x13 grid, with rcut=0.5. It calculates for all the frames of the trajectory, then at the end it finds a number of "hbonds" and 0 different atom-pairs within H-bond distance. At the end, I obtain a range checking error: "Variable y has value 0. It should have been within [ 0 .. 0 ] and the files .xvg, .log and .ndx are created, but the file .xpm is not. If I understand well, the -r2 flag is then absolutely necessary to tell the program that it does not have to treat this as an H-bond search, but as a contact search, right? The -contact flag is not sufficient, alone? 3) If I fix -r 0.5 -r2 0.6, the program starts calculating. It finds the same number as above of "donor" and "acceptor" atoms and starts doing a grid search on a 15x15x11 grid with rcut=0.6. It calculates for all the frames of the trajectory, then at the end it finds a number of "contacts" and a number of different atom-pairs within second cutoff distance. It produces all the files (.xvg, .ndx, .log and .xpm). In this case, the program has indeed calculated the "contacts", instead of the "hbonds". However, I don't understand if it calculates the contacts within a cutoff distance of 0.5 or within a cutoff distance of 0.6 nm. If I change this second value to, say, 1 nm, the number of contacts is still the same, but the number of different atom-pairs increases to 15951, and the grid has different dimensions (9x9x6) In this case, my question is: how the -r2 flag affects the number of contacts to find? (I would like to ask: what is the function of flag -r2? but looking at the gmx-users archive, it seems to me that nobody knows it...and I'm not able to look into the code, as suggested by somebody...) All of the above are valid points. These features have little or no documentation (there is an open redmine issue about this). I find the g_hbond code hopelessly confusing, myself. My final question is, obviously: what is the correct command to provide to obtain what I want, i.e. the number of contacts between the protein and the ligand within a cutoff radius of 0.5 nm? Don't use g_hbond at all. g_mindist -d 0.5 -on -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] several questions about g_hbond -contact
Dear users, I'm using g_hbond with option -contact in order to find the contacts between my protein and a series of ligands, in a radius of 0.5 nm. I made several calculations but I'm quite uncertain about the results, therefore I'm asking you some questions. The command I used is: g_hbond -f my_prot.xtc -s my_prot.tpr -n index.ndx -g logfile.log -num contact_num.xvg -hbn contact.ndx -hbm contact.xpm -contact (for options -r and -r2 see below). Here my questions: 1) I have to indicate two groups when prompted. If I select first "1" (protein) and then "15" (ligand), the program does not find contacts (it calculates, but says "No contacts found"). On the contrary, if I first select "15" and then "1", the program finds contacts. Why? I'm expecting that if an atom of the protein contacts an atom of the ligand, it is a reversible thing, especially because this is not a H-bond in which the different order D-A could affect the results. To proceed with my test, I always selected first "15" and then "1". 2) If I fix only -r 0.5, the program starts calculating. It finds a number of "donor" and "acceptor" atoms and starts doing a grid search on a 18x18x13 grid, with rcut=0.5. It calculates for all the frames of the trajectory, then at the end it finds a number of "hbonds" and 0 different atom-pairs within H-bond distance. At the end, I obtain a range checking error: "Variable y has value 0. It should have been within [ 0 .. 0 ] and the files .xvg, .log and .ndx are created, but the file .xpm is not. If I understand well, the -r2 flag is then absolutely necessary to tell the program that it does not have to treat this as an H-bond search, but as a contact search, right? The -contact flag is not sufficient, alone? 3) If I fix -r 0.5 -r2 0.6, the program starts calculating. It finds the same number as above of "donor" and "acceptor" atoms and starts doing a grid search on a 15x15x11 grid with rcut=0.6. It calculates for all the frames of the trajectory, then at the end it finds a number of "contacts" and a number of different atom-pairs within second cutoff distance. It produces all the files (.xvg, .ndx, .log and .xpm). In this case, the program has indeed calculated the "contacts", instead of the "hbonds". However, I don't understand if it calculates the contacts within a cutoff distance of 0.5 or within a cutoff distance of 0.6 nm. If I change this second value to, say, 1 nm, the number of contacts is still the same, but the number of different atom-pairs increases to 15951, and the grid has different dimensions (9x9x6) In this case, my question is: how the -r2 flag affects the number of contacts to find? (I would like to ask: what is the function of flag -r2? but looking at the gmx-users archive, it seems to me that nobody knows it...and I'm not able to look into the code, as suggested by somebody...) My final question is, obviously: what is the correct command to provide to obtain what I want, i.e. the number of contacts between the protein and the ligand within a cutoff radius of 0.5 nm? Thanks in advance for your suggestions, and best regards Anna __ Anna Marabotti, Ph.D. Web site: http://bioinformatica.isa.cnr.it/anna/anna.htm "When a man with a gun meets a man with a pen, the man with the gun is a dead man" (Roberto Benigni, about Roberto Saviano) -- 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
