[gmx-users] Formatting of spacing in .top and .itp files

[Andrew DeYoung]

Hi,

I am running Gromacs 4.5.5.  In that rather old version, there is a
binary called g_x2top -- I think it is now called something else -- to
generate "a primitive topology from a coordinate file."

When I use g_x2top with my (custom) force field, g_x2top generates a
nicely formatted topology file (either .top or .itp).  Here is a
snippet from the nicely formatted topology (assuming you display the
text in a fixed width font):

[ dihedrals ]
;  ai    aj    ak    al funct            c0            c1
c2            c3            c4            c5
   81    97   113   129     1
  112    97   113   114     1
  112    97   113   129     1
   82    98    99    83     1
   82    98    99   115     1

(Only atom indices and a function type are printed because I used the
option -noparam in g_x2top.)

But, what if I want to generate my own .top or .itp text file, using
for example Fortran, Perl, or Python?  Are .top and .itp fixed-spaced
file formats?  In other words, do I have to nicely align the columns
as g_x2top does?  Or can I just use any number of spaces to delimit
the columns, like in the following example?

[ dihedrals ]
81 97 113 129 1
112 97 113 114 1
112 97 113 129 1
82 98 99 83 1
82 98 99 115 1

I have tried this ugly formatting, and it seems to give the same
results as the nice formatting.  But can anyone confirm that .top and
.itp are NOT fixed-spaced file formats (unlike .pdb and .gro for
example)?

Thanks for your time,
Andrew DeYoung
Carnegie Mellon University