Thank you.<div>I am new to Unix commands, so could you please explain a little more how I am to apply these bug fixes?</div><div><br class="webkit-block-placeholder"></div><div>Thanks<br><br><div class="gmail_quote">On Mon, Nov 9, 2009 at 12:51 PM, Bruce D. Ray <span dir="ltr"><<a href="mailto:brucedray@yahoo.com">brucedray@yahoo.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><div><div style="font-family:times new roman,new york,times,serif;font-size:10pt"><div><span style="font-family:times new roman,new york,times,serif">On </span><font style="font-family:times new roman,new york,times,serif" face="Tahoma" size="2">Sun, November 8, 2009 at 5:31:30 PM, </font><font style="font-family:times new roman,new york,times,serif" face="Tahoma" size="2">Gunnar Widtfeldt Reginsson<br>
<<a href="mailto:reginsson@gmail.com" target="_blank">reginsson@gmail.com</a>> wrote:</font><div><div></div><div class="h5"><br style="font-family:times new roman,new york,times,serif"><br>> I have a small organic molecule that I processed with antechamber
using the gaff forcefield<br>> and got a mol2 file. I want to get .gro and.
itp files from this to use with GROMACS. So I tried<br>> to use the program
"topolbuild version 1.2" from the GROMACS website.</div></div></div><div><div></div><div class="h5">
<div>> <br></div><div>> when I execute the command:</div><div>> "topolbuild -dir ../ -ff gaff -n nameofmolecule -r SL -last 1241 -resnum 40"<br></div><div>>
I get this error message:</div><div>> Fatal error.</div><div>> Source code file: readmol2.c, line: 109</div><div>> Atomic symbol cc in atom type not found.</div><div>> </div><div>> When
I excecute the topolbuild above I use -dir ../ because that should take
the program<br>> to the directory containing dat/antechamber and etc. which
actually comes with the<br>> topolbuild 1.2 package</div>
<div>> </div><div>> I don't know what to do and I have tried searching this mailing list and google without sucess.</div><div>> </div><div>> Can someone please help me?</div></div></div><div><br>First, the mol2 file that you are using is not syntactically correct because it is using<br>
gaff atom types and not Tripos' Sybyl atom types. A syntactically correct mol2 file<br>would not have atom type cc. Please process your organic molecule against the<br>Sybyl force field to get a correct mol2 file.<br>
<br>Second, there are a number of bug fixes I have placed in this list for version 1.2.1<br>which is the version I hope you are using. The following diffs should be applied:<br><br><font size="2"><span style="font-family:Courier New,courier,monaco,monospace,sans-serif">diff topolbuild1_2_1/src/Makefile topolbuild1_2_2/src/Makefile</span><br style="font-family:Courier New,courier,monaco,monospace,sans-serif">
<span style="font-family:Courier New,courier,monaco,monospace,sans-serif">22,23c22,29</span><br style="font-family:Courier New,courier,monaco,monospace,sans-serif"><span style="font-family:Courier New,courier,monaco,monospace,sans-serif">< $(PROGRAM): $(SOURCES)</span><br style="font-family:Courier New,courier,monaco,monospace,sans-serif">
<span style="font-family:Courier New,courier,monaco,monospace,sans-serif">< $(CC) -o $(PROGRAM) $(CFLAGS) $(SOURCES) -lm</span><br style="font-family:Courier New,courier,monaco,monospace,sans-serif"><span style="font-family:Courier New,courier,monaco,monospace,sans-serif">---</span><br style="font-family:Courier New,courier,monaco,monospace,sans-serif">
<span style="font-family:Courier New,courier,monaco,monospace,sans-serif">> $(PROGRAM): $(OBJECTS)</span><br style="font-family:Courier New,courier,monaco,monospace,sans-serif"><span style="font-family:Courier New,courier,monaco,monospace,sans-serif">> $(CC) -o $(PROGRAM) $(CFLAGS) $(OBJECTS) -lm</span><br style="font-family:Courier New,courier,monaco,monospace,sans-serif">
<span style="font-family:Courier New,courier,monaco,monospace,sans-serif">> </span><br style="font-family:Courier New,courier,monaco,monospace,sans-serif"><span style="font-family:Courier New,courier,monaco,monospace,sans-serif">> clean:</span><br style="font-family:Courier New,courier,monaco,monospace,sans-serif">
<span style="font-family:Courier New,courier,monaco,monospace,sans-serif">> rm -f *.o</span><br style="font-family:Courier New,courier,monaco,monospace,sans-serif"><span style="font-family:Courier New,courier,monaco,monospace,sans-serif">> </span><br style="font-family:Courier New,courier,monaco,monospace,sans-serif">
<span style="font-family:Courier New,courier,monaco,monospace,sans-serif">> dist_clean:</span><br style="font-family:Courier New,courier,monaco,monospace,sans-serif"><span style="font-family:Courier New,courier,monaco,monospace,sans-serif">> rm -f *.o $(PROGRAM)</span><br style="font-family:Courier New,courier,monaco,monospace,sans-serif">
<span style="font-family:Courier New,courier,monaco,monospace,sans-serif">diff topolbuild1_2_1/src/Makefile.G4OsX topolbuild1_2_2/src/Makefile.G4OsX</span><br style="font-family:Courier New,courier,monaco,monospace,sans-serif">
<span style="font-family:Courier New,courier,monaco,monospace,sans-serif">22,23c22,29</span><br style="font-family:Courier New,courier,monaco,monospace,sans-serif"><span style="font-family:Courier New,courier,monaco,monospace,sans-serif">< $(PROGRAM): $(SOURCES)</span><br style="font-family:Courier New,courier,monaco,monospace,sans-serif">
<span style="font-family:Courier New,courier,monaco,monospace,sans-serif">< $(CC) -o $(PROGRAM) $(CFLAGS) $(SOURCES) -lm</span><br style="font-family:Courier New,courier,monaco,monospace,sans-serif"><span style="font-family:Courier New,courier,monaco,monospace,sans-serif">---</span><br style="font-family:Courier New,courier,monaco,monospace,sans-serif">
<span style="font-family:Courier New,courier,monaco,monospace,sans-serif">> $(PROGRAM): $(OBJECTS)</span><br style="font-family:Courier New,courier,monaco,monospace,sans-serif"><span style="font-family:Courier New,courier,monaco,monospace,sans-serif">> $(CC) -o $(PROGRAM) $(CFLAGS) $(OBJECTS) -lm</span><br style="font-family:Courier New,courier,monaco,monospace,sans-serif">
<span style="font-family:Courier New,courier,monaco,monospace,sans-serif">> </span><br style="font-family:Courier New,courier,monaco,monospace,sans-serif"><span style="font-family:Courier New,courier,monaco,monospace,sans-serif">> clean:</span><br style="font-family:Courier New,courier,monaco,monospace,sans-serif">
<span style="font-family:Courier New,courier,monaco,monospace,sans-serif">> rm -f *.o</span><br style="font-family:Courier New,courier,monaco,monospace,sans-serif"><span style="font-family:Courier New,courier,monaco,monospace,sans-serif">> </span><br style="font-family:Courier New,courier,monaco,monospace,sans-serif">
<span style="font-family:Courier New,courier,monaco,monospace,sans-serif">> dist_clean:</span><br style="font-family:Courier New,courier,monaco,monospace,sans-serif"><span style="font-family:Courier New,courier,monaco,monospace,sans-serif">> rm -f *.o $(PROGRAM)</span><br style="font-family:Courier New,courier,monaco,monospace,sans-serif">
<span style="font-family:Courier New,courier,monaco,monospace,sans-serif">diff topolbuild1_2_1/src/ring_detect.c topolbuild1_2_2/src/ring_detect.c</span><br style="font-family:Courier New,courier,monaco,monospace,sans-serif">
<span style="font-family:Courier New,courier,monaco,monospace,sans-serif">450c450</span><br style="font-family:Courier New,courier,monaco,monospace,sans-serif"><span style="font-family:Courier New,courier,monaco,monospace,sans-serif">< ar_set[(t_ring_atomno[i][j])][3]++;</span><br style="font-family:Courier New,courier,monaco,monospace,sans-serif">
<span style="font-family:Courier New,courier,monaco,monospace,sans-serif">---</span><br style="font-family:Courier New,courier,monaco,monospace,sans-serif"><span style="font-family:Courier New,courier,monaco,monospace,sans-serif">> ar_set[(t_ring_atomno[i][k])][3]++;</span><br style="font-family:Courier New,courier,monaco,monospace,sans-serif">
<span style="font-family:Courier New,courier,monaco,monospace,sans-serif">diff topolbuild1_2_1/src/topolbuild.c topolbuild1_2_2/src/topolbuild.c</span><br style="font-family:Courier New,courier,monaco,monospace,sans-serif">
<span style="font-family:Courier New,courier,monaco,monospace,sans-serif">440c440</span><br style="font-family:Courier New,courier,monaco,monospace,sans-serif"><span style="font-family:Courier New,courier,monaco,monospace,sans-serif">< max_rng =
num_bonds/2;</span><br style="font-family:Courier New,courier,monaco,monospace,sans-serif"><span style="font-family:Courier New,courier,monaco,monospace,sans-serif">---</span><br style="font-family:Courier New,courier,monaco,monospace,sans-serif">
<span style="font-family:Courier New,courier,monaco,monospace,sans-serif">> max_rng = 3 * num_bonds/4;</span><br style="font-family:Courier New,courier,monaco,monospace,sans-serif"></font><br>Also, when using Gromacs force fields, the defaults definition line needs to<br>
be changed from:<br> 1 2 yes 0.5 0.8333<br>to:<br>
1 1 no 1.0 1.0<br><br>Unfortunately, I did not allow for different defaults for different force fields<br>in that version. The next version will correct that as well as adding OPLSAA<br>
to the suite of force fields available.<br><br><br>Sincerely,<br><br><br></div>-- <br>Bruce D. Ray, Ph.D.<br>Associate Scientist<br>IUPUI<br>Physics Dept.<br>402 N. Blackford St.<br>Indianapolis, IN 46202-3273<div><br></div>
</div><br>
</div><br>--<br>
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