[gmx-users] query regarding mk_angndx

[Dallas Warren]

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
dallas.warren at monash.edu
+61 3 9903 9304
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble a nail. 


> -----Original Message-----
> From: gmx-users-bounces at gromacs.org [mailto:gmx-users-
> bounces at gromacs.org] 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 <hmkvsri at gmail.com>
> Date: Fri, Mar 8, 2013 at 10:45 PM
> Subject: query regarding mk_angndx
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> 
> 
> 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
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