To see how the dihedral is defined you need to look at the topology file, not the coordinate file.
Additionally, the name for the index group tells you the type of dihedral. Be careful with that, especially if you are interested in a particular bond and there is another dihedral within the system/molecule that has the same parameters as the script will group them together into one if you are not careful. Catch ya, Dr. Dallas Warren Drug Discovery Biology Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 [email protected] +61 3 9903 9304 --------------------------------- When the only tool you own is a hammer, every problem begins to resemble a nail. > -----Original Message----- > From: [email protected] [mailto:gmx-users- > [email protected]] On Behalf Of Kavyashree M > Sent: Sunday, 10 March 2013 2:09 AM > To: Discussion list for GROMACS users > Subject: [gmx-users] query regarding mk_angndx > > ---------- Forwarded message ---------- > From: Kavyashree M <[email protected]> > Date: Fri, Mar 8, 2013 at 10:45 PM > Subject: query regarding mk_angndx > To: Discussion list for GROMACS users <[email protected]> > > > Dear users, > > I used mkang_ndx to create an index file with dihedral angles. > Input was: > mk_angndx -s a.tpr -n angle.ndx -type dihedral > output angle.ndx read like this - > [ Phi=180.0_2_43.93 ] > 5 20 18 19 22 37 35 36 27 32 30 > 31 > 39 59 57 58 61 76 74 75 66 71 69 > 70 > ... > > According to my understanding the numbers indicate the 4 atoms > defining the particular dihedral angle. > But when I checked the pdb file for these atoms- > ATOM 5 CA MET A 1 111.430 40.170 113.130 1.00 0.00 > ATOM 18 C MET A 1 112.060 41.020 112.030 1.00 0.00 > ATOM 19 O MET A 1 111.910 42.240 112.010 1.00 0.00 > ATOM 20 N GLN A 2 112.940 40.430 111.220 1.00 0.00 > > I could not make out how this defines phi? > Kindly clarify my confusion. > > Thank you > kavya > -- > gmx-users mailing list [email protected] > 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 [email protected]. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list [email protected] 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 [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
