Hi, I used the following command.. gmx mindist -f ../traj_comp3.xtc -s ../md3.tpr -n index.ndx -od minidist.xvg -on numb_count -d 0.65 By doing this I got this numb_count.xvg graph here
https://drive.google.com/open?id=0B99qIEZlZSXfVnQxY3JsUm1rRnc In this number of contacts varying up to 500 which is impossible for my small peptide chain ( two chains in a simulation box and both are seven residue long ). From this I concluded that may be number is so high, because in command line -d 0.65 is not the COM distance. So than I used this gmx select -f ../traj_comp3.xtc -s ../md3.tpr -n index.ndx -select 'group "sd-1" and within 0.65 of com of group "sd-2"' -os size.xvg Where group sd-1 and sd-2 are the side-chain atom index for 1st and 2nd peptide chain. The output by this command is in below link https://drive.google.com/open?id=0B99qIEZlZSXfRDlXN3RaVFROc2s here, output is a size.xvg file which is looking something feasible. I am not sure is that output contains number of inter peptide contacts which I needed or this is something else as the name suggested "size.xvg". Please clear my confusion. Thank you! Sundari On Wed, Jun 28, 2017 at 6:55 AM, Dallas Warren <dallas.war...@monash.edu> wrote: > First thing you should do when asking for help, is specify exactly > what you have have done (that includes the command line and output), > and then why it is "wrong result". > Catch ya, > > Dr. Dallas Warren > Drug Delivery, Disposition and Dynamics > Monash Institute of Pharmaceutical Sciences, Monash University > 381 Royal Parade, Parkville VIC 3052 > dallas.war...@monash.edu > --------------------------------- > When the only tool you own is a hammer, every problem begins to resemble a > nail. > > > On 28 June 2017 at 01:27, Sundari chaudhary <sundi6...@gmail.com> wrote: > > Dear all, > > > > I want to calculate the number of inter-peptide and intra-peptide > > side-chain–side-chain contacts and the criteria to form a contact is > that: > > the distance between the centers of mass of two residues is less than a > > specified distance. I tried gmx mindist and gmx distance command lines > but > > i got wrong results. > > > > Please suggest me right command line to do this analysis. > > > > > > Thank you! > > > > Sundari > > -- > > 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.
