[gmx-users] problem with installation of topolbuild1.2.1

[Bruce D. Ray]

On Wednesday, July 8, 2009 2:32:53 AMsubarna thakur <thakur.subarna at yahoo.co.in> wrote:



> Can anybody please tell me how to install topolbuild 1.2.1
programm in  32 bit machine with
> Fedora linux operating system. I
cannot understand the instruction given in the READ ME file
Apparently some versions of make do not handle my make files the same way that
the version of make I use does.  to correct this, replace the file in src named Makefile
with the attached version.

Second, to allow larger memory allocation for recursive ring detection in
some complicated ring systems, the estimate of maximum number of rings
needs to be increased.  In the source code, in file topolbuild.c, change the
following line:

     max_rng = num_bonds/2;
to
     max_rng = 3 * num_bonds/4;

Third, to correct for an error in setting a ring type flag, in file ringdetect.c,
function aromaticity 
change
                                        ar_set[(t_ring_atomno[i][j])][3]++;
to
                                        ar_set[(t_ring_atomno[i][k])][3]++;

 
Then type make to compile.

Once the program is compiled, you can relocate the executable, named
topolbuild, and the entire dat directory where you wish them to be.
Items in the water_and_ions directory need to be placed where grompp
can find them.


Sincerely,


-- 
Bruce D. Ray, Ph.D.
Associate Scientist, and Operations Director
NMR Center
IUPUI
Physics Dept.
402 N. Blackford St.
Indianapolis, IN  46202-3273


      
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