On 4/12/18 2:12 PM, Andrew DeYoung wrote:
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)?
GROMACS topologies are free format.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com
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