[gmx-users] make_ndx may contain a bug?

Paul Barrett barrett at biop.ox.ac.uk
Thu May 1 15:24:00 CEST 2003

Possible bug found in use of make_ndx. Sorry if it is just a mistake on
my part...


1) I made an index file from a protein with 298 residues.
make_ndx correctly reported the following:

  1 Protein             :  3054 atoms
  2 Protein-H           :  2398 atoms
  3 C-alpha             :   298 atoms

2) I changed one residue in the protein to a non-standard residue. (I
changed THR to TPO which I had defined elsewhere to be a phosphorylated

make_ndx came up with 

  1 Protein             :  3045 atoms
  2 Protein-H           :  2391 atoms
  3 C-alpha             :   297 atoms

Which is correct (although not what I wanted!) because TPO is not
defined as an amino acid so its carbon cannot be a C-alpha.

3) To fix this I added residue name TPO into aminoacids.dat and
incremented the line count at the top of the file. make_ndx now
correctly identified TPO as part of the protein so gave output again
exactly like (1) i.e. with 298 C-alphas. So far so good.


4) then I added a comment line in aminoacids.dat so that locally it
looks like...

TPO  ; this is phosphorylated threonine

and now make_ndx comes up with...

  1 Protein             :  2609 atoms
  2 Protein-H           :  2065 atoms
  3 C-alpha             :   261 atoms

It is omitting residues.


1) I cannot spot a pattern in which residues it is missing out: it is
not just one kind (nor even just those from the tail of aminoacids.dat)
2) most wierdly the value of C-alpha from make_ndx varies with the
contents of the comment! e.g.

COMMENT                             |       REPORTED C-ALPHA
(none)                              |            298
; this                              |            275
; this is                           |            265
; this is phosphorylated            |            261
; this is phosphorylated threonine  |            261
; (as above + 20 more characters)   |            261

I can carry on and make my simulation work but this is a nasty trap (in
a great program) that could easily catch people unawares.
3) there are other comment lines in the .dat file that do not cause

many thanks

Paul Barrett

More information about the gromacs.org_gmx-users mailing list