[gmx-users] topolbuild cannot open logfile
Bruce D. Ray
brucedray at yahoo.com
Wed Sep 29 14:07:12 CEST 2010
On Tue, September 28, 2010 at 7:38 PM, "andrew_m_norris at talk21.com"
<andrew_m_norris at talk21.com> wrote:
> Hello i am very new to molecular mechanics so please excuse me if my
> questions are a little naive or stupid.
> I am trying to minimise a mol2 file with topolbuild1_3 using the following
> command line arguments from within the topolbuild directory:
> ./topolbuild -dir /usr/local/gromacs/share/gromacs/top -ff oplsaa
>-n /Users/bioinformatics/Desktop/zinc_12404782 -purge 0 -move
> I get the following error:
> Fatal error.
> Source code file: topolbuild.c, line: 345
> Cannot open log file zinc_12404782.log
> I realise that i will have to go over the parameters again but i was hoping
>for some sort of output.
> Does anyone know if it is a problem with the parameters of the input file
>shown below or some
> problem with the way in which topolbuild is called ? I am a little unsure how
>to point to the
> oplsaa force fields?
The problem with your command is that you do not have write permission in the
in which topolbuild resides. You need to run the command from the directory in
you want the topology built with a command such as:
/path-to-topolbuild-main-directory/dat/gromacs -ff oplsaa -n
/Users/bioinformatics/Desktop/zinc_12404782 -purge 0 -move
Note that the gromacs directory does not contain the topolbuild tables.
Please see the examples given in the PROGRAM_TESTING_DONE.txt file in the
topolbuild distribution for more information.
Bruce D. Ray, Ph.D.
402 N. Blackford St.
Indianapolis, IN 46202-3273
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