Thanks very much for your reply yes i was just being daft and trying to run
things from the wrong place therefore wrong permissions! Also i was pointing to
the wrong directory for force fields. Things are working now.
Thank you once again Andrew
--- On Wed, 29/9/10, Bruce D. Ray <bruced...@yahoo.com> wrote:
From: Bruce D. Ray <bruced...@yahoo.com>
Subject: Re: [gmx-users] topolbuild cannot open logfile
To: gmx-users@gromacs.org
Date: Wednesday, 29 September, 2010, 13:07
On Tue, September 28, 2010 at 7:38 PM, "andrew_m_nor...@talk21.com"
<andrew_m_nor...@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
directory
in which topolbuild resides. You need to run the command from the directory in
which
you want the topology built with a command such as:
/path-to-topolbuild-main-directory/src/topolbuild -dir
/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.
Associate Scientist
IUPUI
Physics Dept.
402 N. Blackford St.
Indianapolis, IN 46202-3273
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