Re: [gmx-users] HYDROGEN BOND EXISTENCE MAP
Thanks. On Sat, Apr 1, 2017 at 12:59 PM, Sheeja Vasudevanwrote: > > Hi Neha, > > If I understand correctly pdb file is used for extracting information > about the topology of the molecule..in this case the atom name and type. > so it does not matter at which time point of time in your simulation your > pdb file is generated as long as it is whole molecule. > > Best > Sheeja. > > > Hi gromacs users, > > > > In the perl script to calculate hydrogen bond %, the command is > > > > perl plot_hbmap.pl -s structure.pdb -map hbmap.xpm -index hbond.ndx > > > > > > What should the structure.pdb file contain? > > > > How to obtain it? > > > > At which point of simulations? > > > > Thanks, > > Neha > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send > > a mail to gmx-users-requ...@gromacs.org. > > > > > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/ > Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] HYDROGEN BOND EXISTENCE MAP
Hi Neha, If I understand correctly pdb file is used for extracting information about the topology of the molecule..in this case the atom name and type. so it does not matter at which time point of time in your simulation your pdb file is generated as long as it is whole molecule. Best Sheeja. > Hi gromacs users, > > In the perl script to calculate hydrogen bond %, the command is > > perl plot_hbmap.pl -s structure.pdb -map hbmap.xpm -index hbond.ndx > > > What should the structure.pdb file contain? > > How to obtain it? > > At which point of simulations? > > Thanks, > Neha > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send > a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] HYDROGEN BOND EXISTENCE MAP
Hi gromacs users, In the perl script to calculate hydrogen bond %, the command is perl plot_hbmap.pl -s structure.pdb -map hbmap.xpm -index hbond.ndx What should the structure.pdb file contain? How to obtain it? At which point of simulations? Thanks, Neha -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Hydrogen bond existence map
Hi all I would like to create hydrogen bond existence map for interaction of each residue with my ligand. I am aware that -hbm and -hbn option of g_hbond along with index file would serve the purpose. But the resulting output file is giving existence map for each atom of the residue. Instead, I want one map for residue as a whole. Example if any residue of protein is forming hydrogen bond with my ligand for certain time through bond A but for the remaining time it forms through bond B, then I want the map to show presence of hydrogen bond through one single line during the entire course of simulation. Is it possible with gromacs? Thanks in advance Nidhi -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Hydrogen bond existence map
Hi Nidhi, Only with post processing of named files I'm afraid. Kind regards, Erik On 19 Jun 2014, at 10:48, Nidhi Katyal nidhikatyal1...@gmail.com wrote: Hi all I would like to create hydrogen bond existence map for interaction of each residue with my ligand. I am aware that -hbm and -hbn option of g_hbond along with index file would serve the purpose. But the resulting output file is giving existence map for each atom of the residue. Instead, I want one map for residue as a whole. Example if any residue of protein is forming hydrogen bond with my ligand for certain time through bond A but for the remaining time it forms through bond B, then I want the map to show presence of hydrogen bond through one single line during the entire course of simulation. Is it possible with gromacs? Thanks in advance Nidhi -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.