[gmx-users] topolbuild cannot open logfile

andrew_m_norris at talk21.com andrew_m_norris at talk21.com
Wed Sep 29 14:54:04 CEST 2010

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 <brucedray at yahoo.com> wrote:

From: Bruce D. Ray <brucedray at yahoo.com>
Subject: Re: [gmx-users] topolbuild cannot open logfile
To: gmx-users at gromacs.org
Date: Wednesday, 29 September, 2010, 13:07

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
> questions are a little naive or stupid.> I
 am trying to minimise a mol2 file with topolbuild1_3 using the 
> 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
> 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
Physics Dept.
402 N. Blackford St.
Indianapolis, IN  46202-3273

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