<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><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="Apple-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="Apple-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="Apple-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="Apple-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="Apple-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="Apple-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="Apple-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; font-size:
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