<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;">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.<div><br></div><div>Thank you once again Andrew<br><br>--- On <b>Wed, 29/9/10, Bruce D. Ray <i><brucedray@yahoo.com></i></b> wrote:<br><blockquote style="border-left: 2px solid rgb(16, 16, 255); margin-left: 5px; padding-left: 5px;"><br>From: Bruce D. Ray <brucedray@yahoo.com><br>Subject: Re: [gmx-users] topolbuild cannot open logfile<br>To: gmx-users@gromacs.org<br>Date: Wednesday, 29 September, 2010, 13:07<br><br><div id="yiv1070136629"><style type="text/css"><!--#yiv1070136629 DIV {margin:0px;}--></style><div style="font-family:Courier New, courier, monaco, monospace, sans-serif;font-size:10pt;"><font style="font-family:times new
roman, new york, times, serif;" size="2"><span class="yiv1070136629Apple-style-span" style="font-size:medium;"></span></font><font style="font-family:times new roman, new york, times, serif;" size="2">On Tue, September 28, 2010 at 7:38 PM</font><font size="2"><span style="font-family:times new roman, new york, times, serif;">, </span></font><font style="font-family:times new roman, new york, times, serif;" size="2">"andrew_m_norris@talk21.com" <andrew_m_norris@talk21.com> wrote:</font><font size="2"><br style="font-family:times new roman, new york, times, serif;"></font><font style="font-family:times new roman, new york, times, serif;" size="2"><span class="yiv1070136629Apple-style-span" style="font-size:medium;">> Hello i am very new to molecular mechanics so please excuse me if
my<br>> questions are a little naive or stupid.</span></font><div style="font-family:times new roman, new york, times, serif;font-size:medium;"><font size="2">> I
am trying to minimise a mol2 file with topolbuild1_3 using the
following<br>> command line arguments from within the topolbuild directory:</font></div><div style="font-family:times new roman, new york, times, serif;font-size:medium;"><font size="2"><br></font></div><font style="font-family:times new roman, new york, times, serif;" size="2"><span class="yiv1070136629Apple-style-span" style="border-collapse:collapse;font-size:13px;line-height:15px;"><div style="margin:0px;padding:0px;line-height:1.2em;outline-style:none;font-family:Courier New, courier, monaco, monospace, sans-serif;"><font size="1">> ./topolbuild
-dir /usr/local/gromacs/share/gromacs/top -ff oplsaa
-n /Users/bioinformatics/Desktop/zinc_12404782 -purge 0 -move</font></div><div style="margin:0px;padding:0px;line-height:1.2em;outline-style:none;">><br></div><div style="margin:0px;padding:0px;line-height:1.2em;outline-style:none;">> I get the following error:</div><div style="margin:0px;padding:0px;line-height:1.2em;outline-style:none;">> <br></div><div style="margin:0px;padding:0px;line-height:1.2em;outline-style:none;">> Fatal error.</div><div style="margin:0px;padding:0px;line-height:1.2em;outline-style:none;"><font style="font-family:times new roman, new york, times, serif;" size="2"><span class="yiv1070136629Apple-style-span" style="border-collapse:collapse;font-size:13px;line-height:15px;">> </span></font>Source code file: topolbuild.c, line: 345</div><div style="margin:0px;padding:0px;line-height:1.2em;outline-style:none;"><font style="font-family:times new roman, new york, times, serif;" size="2"><span
class="yiv1070136629Apple-style-span" style="border-collapse:collapse;font-size:13px;line-height:15px;">> </span></font>Cannot open log file zinc_12404782.log</div><div style="margin:0px;padding:0px;line-height:1.2em;outline-style:none;"><font style="font-family:times new roman, new york, times, serif;" size="2"><span class="yiv1070136629Apple-style-span" style="border-collapse:collapse;font-size:13px;line-height:15px;">> </span></font></div><div style="margin:0px;padding:0px;line-height:1.2em;outline-style:none;"><font style="font-family:times new roman, new york, times, serif;" size="2"><span class="yiv1070136629Apple-style-span" style="border-collapse:collapse;font-size:13px;line-height:15px;">> </span></font>I
realise that i will have to go over the parameters again but i was
hoping for some sort of output.<br>> Does anyone know if it is a problem with
the parameters of the input file shown below or some<br>> problem with the
way in which topolbuild is called ? I am a little unsure how to point to
the<br>> oplsaa force fields? <br></div></span></font><div><font size="2"><span style="font-family:times new roman, new york, times, serif;"> </span><br style="font-family:times new roman, new york, times, serif;"></font><span style="font-family:times new roman, new york, times, serif;"><font size="2"><span style="font-family:times new roman, new york, times, serif;">The problem with your command is that you do not have write permission in the directory</span><br style="font-family:times new roman, new york, times, serif;"><span style="font-family:times new roman, new york, times, serif;">in which topolbuild resides. You need to run the command from the directory in which</span><br style="font-family:times new roman, new york, times, serif;"><span style="font-family:times new roman, new york, times, serif;">you want the topology built with a command such as:</span><br style="font-family:times new roman, new york, times, serif;"><br
style="font-family:times new roman, new york, times, serif;"></font><font style="font-family:Courier New, courier, monaco, monospace, sans-serif;" size="1">/path-to-topolbuild-main-directory/src/topolbuild -dir </font></span><font style="font-family:Courier New, courier, monaco, monospace, sans-serif;" size="1">/path-to-topolbuild-main-directory/dat/gromacs -ff oplsaa -n /Users/bioinformatics/Desktop/zinc_12404782 -purge 0 -move<br></font><font style="font-family:Courier New, courier, monaco, monospace, sans-serif;" size="1"><br></font><span style="font-family:times new roman, new york, times, serif;">Note that the gromacs directory does not contain the topolbuild tables.<br>Please see the examples given in the PROGRAM_TESTING_DONE.txt file in the<br>topolbuild distribution for more information.<br><br style="font-family:times new roman, new york, times, serif;"></span></div><span style="font-family:times new roman, new york, times, serif;">--
</span><br style="font-family:times new roman, new york, times, serif;"><span style="font-family:times new roman, new york, times, serif;">Bruce D. Ray, Ph.D.</span><br style="font-family:times new roman, new york, times, serif;"><span style="font-family:times new roman, new york, times, serif;">Associate Scientist</span><br style="font-family:times new roman, new york, times, serif;"><span style="font-family:times new roman, new york, times, serif;">IUPUI</span><br style="font-family:times new roman, new york, times, serif;"><span style="font-family:times new roman, new york, times, serif;">Physics Dept.</span><br style="font-family:times new roman, new york, times, serif;"><span style="font-family:times new roman, new york, times, serif;">402 N. Blackford St.</span><br style="font-family:times new roman, new york, times, serif;"><span style="font-family:times new roman, new york, times, serif;">Indianapolis, IN 46202-3273<br><br></span><div
style="font-family:Courier New, courier, monaco, monospace, sans-serif;
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