[gmx-users] Topolbuild configuration

Bruce D. Ray brucedray at yahoo.com
Mon Dec 10 14:26:16 CET 2012

On Sunday, December 9, 2012 at 7:48 PM SeokYun123 <kimseokyun3 at gmail.com> wrote:

>I'm trying to download topolbuild1_2_1 in my Mac computer.

First, why are you using 1.2.1 instead of 1.3 which is also available in the user
contributed software section at gromacs.org?  Actually, there should be a
topolbuild1_3_1 contribution there as well.  I don't know what happened
to that release.  Actually, topolbuild is not up to date with gromacs releases.

>I understand that the executable file is in the same directory as the
>Makefile. I also understand the thing about the PATH.

Did you read INSTALLATION.txt in the main directory?

>For different files I have downloaded, I was able to ./configure it and use
>make, but for topolbuild, I wasn't able to ./configure it as it prints out
>an error message.

This is because there isn't a configure script at all for topolbuild
Instead some sample makefiles are provided named Makefile
and Makefile.G4OsX  For your purposes, the supplied Makefile
should work so you just need to type make to get an executable.
Type make clean to clean up afterwards.

>From the previous thread, I read that "Common practice is to then put it in
>some central directory for executables (like /usr/local/bin, or some
>subdirectory of your /home directory, depending on
>your permissions on the system)." 

You can either leave the executable in the src directory where it is built,
or you can move it to a desired directory.  Please remember that the dat
directory contains the parameters files that topolbuild needs in order to
generate a topology.

>I think that would help me fix my problem, but I'm not so sure how to do
>Could anyone give me an advice regarding this issue?

There are  *.txt files in the main directory of each version of topolbuild to
document how to install and how to use the program.  Please remember
that the topologies generated need further editing with a text editor for use
with gromacs 4.5 and 4.6 releases because the organization of topology files
changed with the 4.5 release and topolbuild has not been updated in a while.

Bruce D. Ray, Ph.D.
Associate Scientist
Physics Dept.
402 N. Blackford St.
Indianapolis, IN  46202-3273


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