Thank you. It worked now. Best Francesca
2012/2/29 Mark Abraham <mark.abra...@anu.edu.au>: > On 1/03/2012 1:00 AM, francesca vitalini wrote: >> >> Hi Mark, >> Thanks for your answer. What I'm trying to do is calculate the value >> in degrees of the angles listed in my index file. If my index file >> looks like >> [ dihedral 1 ] >> 2 7 9 10 >> [ dihedral 2 ] >> 10 16 18 19 > > > I said in my last email that my suggestion of a separate group group for > each angle was wrong and that your original index file like > > > [ dihedrals ] > 2 5 9 10 > 10 15 18 19 > ..... > > was fine. Please try that with g_angle -ov -all. I get output like > > # This file was created Mon Feb 20 12:32:15 2012 > > # by the following command: > # g_angle -f 005_5 -type dihedral -all -ov 005_5_angles.xvg -n > ../1oei_sim_backbone_angle.ndx > # > # g_angle is part of G R O M A C S: > # > # GRoups of Organic Molecules in ACtion for Science > # > @ title "Average Angle: Backbone_dihedral_angles" > @ xaxis label "Time (ps)" > @ yaxis label "Angle (degrees)" > @TYPE xy > 245757.00000 19.937 1.923 -61.394 -74.236 27.453 -2.719 > -179.194 96.730 -27.468 43.121 -8.608 -0.480 -0.764 > 0.001 -179.750 170.982 157.245 -174.933 37.563 40.854 93.329 > 19.823 169.543 129.371 40.443 -149.558 8.198 43.427 > 100.089 86.565 154.344 171.804 52.401 -158.571 27.166 > -143.253 39.944 6.985 178.488 179.865 -0.432 179.965 > -179.957 179.499 -179.774 -179.788 107.176 151.312 -37.770 > 245762.00000 22.309 -1.821 -60.416 -73.830 -21.904 -2.231 > -179.111 96.693 -114.414 40.600 -154.543 0.922 -2.143 > 0.932 179.704 -71.467 147.204 171.571 52.328 39.069 70.499 > 3.113 179.355 91.086 43.155 133.656 -22.505 23.643 > 104.997 105.160 151.335 -176.456 176.378 23.691 6.447 -102.512 > 43.837 33.328 -179.572 -179.286 1.288 179.801 179.207 > -179.029 -178.575 179.950 151.692 164.967 -4.967 > 245763.00000 36.760 -1.567 -59.734 -74.259 -88.956 9.191 > 175.880 91.328 -106.962 38.466 -159.767 -0.092 1.363 > -0.665 -179.743 -63.435 159.398 168.167 42.926 40.201 > 86.058 15.792 171.260 108.564 37.481 148.734 -19.163 > 41.603 95.716 100.927 159.081 177.076 170.625 18.814 > 11.879 -108.608 42.251 31.301 -179.193 -179.047 0.401 > -179.484 179.431 179.957 179.578 179.770 143.532 159.744 > -1.341 > > > Mark > > >> then if I use the command line >> >> g_angle -f aa.gro -s aa.tpr -n angles_prova.ndx -ov angav_prova3.xvg >> -all -type dihedral >> or the same with the flag -od, >> what I get is an interactive menu where I have to choose the group and >> if I choose one then I obtain an output file which looks like >> # This file was created Wed Feb 29 14:54:55 2012 >> # by the following command: >> # /home/cocktail/vitalini/gromacs_special/bin/g_angle -f aa.gro -s >> aa.tpr -n angles_prova.ndx -od angav_prova3.xvg -all -type dihedral >> # >> # /home/cocktail/vitalini/gromacs_special/bin/g_angle is part of G R O M A >> C S: >> # >> # Great Red Oystrich Makes All Chemists Sane >> # >> @ title "Dihedral Distribution: dihedral" >> @ xaxis label "Degrees" >> @ yaxis label "" >> @TYPE xy >> @ subtitle "average angle: -6192.3\So\N" >> -109 0.000000 >> -108 1.000000 >> -107 0.000000 >> >> Which does what I'm looking for but this means that I'll need a file >> for each angle. Is there a faster way to get a file that has like two >> columns, one for the dihedral and another one for the angles? >> Thanks >> Francesca >> >> 2012/2/29 Mark Abraham<mark.abra...@anu.edu.au>: >>> >>> On 29/02/2012 11:54 PM, francesca vitalini wrote: >>>> >>>> 2012/2/29 Mark Abraham<mark.abra...@anu.edu.au>: >>>>> >>>>> On 29/02/2012 9:39 PM, francesca vitalini wrote: >>>>>> >>>>>> Hi all, >>>>>> I'm trying to use g_angle to calculate a list of dihedrals that I have >>>>>> into an hand made index file (angles.ndx), which looks like >>>>>> [ dihedrals ] >>>>>> 2 5 9 10 >>>>>> 10 15 18 19 >>>>>> ..... >>>>> >>>>> >>>>> mk_angndx might have helped. >>>> >>>> Actually mk_angndx gies me the angles for phi and psi while instead I >>>> need omega and they are put in a strange format like in groups of 8 >>>> instead of 4. >>> >>> >>> Whitespace inside the index group probably doesn't matter. >>> >>> >>>>>> However it produces a .xvg file where it gives me for each angle in >>>>>> degrees its probability. However, what I want is instead to know the >>>>>> value in degrees of each angle in the ndx file. Do you have any >>>>>> suggestions apart from building an index file for each angle? >>>>> >>>>> >>>>> g_angle -ov -all with each angle in its own group. >>>> >>>> What do you mean with each angle in its own group? something like >>>> [dihedrals] >>>> 2 5 9 10 >>>> [dihedrals] >>>> 10 13 16 18 >>>> ... >>> >>> >>> Yes, but with unique group names - but it turns out I was wrong to >>> suggest >>> that. Your index file above is fine. >>> >>> >>>> Isn't it equivalent to build differend index files? >>>> anyway the -ov flag gives the average over time, but I need the angles >>>> just at one time, that is why I was using -od but it just plots the >>>> distribution of all angles together. >>>> Any help? >>> >>> >>> Which part of the output of g_angle -ov **-all** doesn't suit you? >>> >>> Mark >>> >>> >>>> Thanks >>>> >>>>> Mark >>>>> -- >>>>> gmx-users mailing list gmx-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 mailing list gmx-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 mailing list gmx-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 -- Francesca Vitalini PhD student at Computational Molecular Biology Group, Department of Mathematics and Informatics, FU-Berlin Arnimallee 6 14195 Berlin vital...@zedat.fu-berlin.de francesca.vital...@fu-berlin.de +49 3083875776 +49 3083875412 -- gmx-users mailing list gmx-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
