I used gzip to uncompress the file first:<br><br># gzip -d topolbuild1_2_1.tgz<br><br>and then I used tar:<br><br># tar -xvf topolbuild1_2_1.tar<br><br>This seems to work.<br><br><br><br><br><br><div class="gmail_quote">On Sat, Aug 1, 2009 at 6:05 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div class="im"><br>
<br>
Nancy wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hello,<br>
<br>
I downloaded "topolbuild1_2_1.tgz" from the URL: <a href="http://www.gromacs.org/@api/deki/files/40/=topolbuild1_2_1.tgz" target="_blank">http://www.gromacs.org/@api/deki/files/40/=topolbuild1_2_1.tgz</a><br>
<br>
However, when I tried to decompress the file, I received the following error message:<br>
<br>
# tar -xvf topolbuild1_2_1.tgz<br>
</blockquote>
<br></div>
You have to unzip it as well, i.e.:<br>
<br>
tar -zxvf topolguild1_2_1.tgz<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div class="im">
tar: This does not look like a tar archive<br>
tar: Skipping to next header<br>
tar: Archive contains obsolescent base-64 headers<br>
tar: Error exit delayed from previous errors<br>
<br>
I also tried to obtain topolbuild 1.2.1 from<br>
<br>
<a href="http://oldwww.gromacs.org/component/option,com_docman/task,doc_download/gid,111/Itemid,26/" target="_blank">http://oldwww.gromacs.org/component/option,com_docman/task,doc_download/gid,111/Itemid,26/</a><br>
<br>
but that did not work either. Please advise.<br>
<br>
Thank you.<br>
Nancy<br>
<br>
<br>
<br></div><div class="im">
On Sat, Aug 1, 2009 at 11:31 AM, Bruce D. Ray <<a href="mailto:brucedray@yahoo.com" target="_blank">brucedray@yahoo.com</a> <mailto:<a href="mailto:brucedray@yahoo.com" target="_blank">brucedray@yahoo.com</a>>> wrote:<br>
<br>
On Fri, Jul 31, 2009 at 5:19:19 PM, Nancy <<a href="mailto:nancy5villa@gmail.com" target="_blank">nancy5villa@gmail.com</a><br></div><div><div></div><div class="h5">
<mailto:<a href="mailto:nancy5villa@gmail.com" target="_blank">nancy5villa@gmail.com</a>>> wrote:<br>
> If it necessary to manually create force field parameters for<br>
each molecule, then how can one run a<br>
> simulation involving a number of arbitrary molecules (e.g. a set<br>
of mono and disaccharides) for<br>
> which there are no existing force fields?<br>
><br>
> Do you know of any other MD software package that is capable of<br>
running simulations on<br>
> arbitrary molecules without having to "piece together" a force<br>
field for each molecule?<br>
<br>
Provided that the desired force field has suitable parameters for a<br>
particular bonding situation<br>
already, there are software packages that can generate a potentially<br>
suitable topology from<br>
a molecule's structure. For gromacs topologies, user contributions<br>
to gromacs include<br>
topolbuild 1.2.1 that supports amber, gaff, glycam, Tripos, and<br>
gromacs force fields<br>
(my upcoming version 1.3 will also do OPLS-AA with the numeric opls<br>
atom types), and<br>
topolgen 1.1, a Perl script that supports OPLS-AA. Also available<br>
in user contributions<br>
is ambconv that takes the file generated by antechamber and leap<br>
from amber tools<br>
and generates a gromacs topology that uses the amber or gaff<br>
forcefield selected when<br>
leap was applied to the antechamber output. Another option is the<br>
Perl script<br>
mktop at <<a href="http://labmm.iq.ufrj.br/mktop/" target="_blank">http://labmm.iq.ufrj.br/mktop/</a>>, documented in Ribeiro,<br>
A.A.S.T., Horta, B.A.C.,<br>
and de Alencastro, R.B. J. Braz. Chem. Soc., Vol. 19, No. 7,<br>
1433-1435, 2008. Also<br>
there is acpypi, the AnteChamber Python Parser Interface available at<br></div></div>
<<a href="http://code.google.com/p/acpypi/" target="_blank">http://code.google.com/p/acpypi/</a>>./ <<a href="http://code.google.com/p/acpypi/" target="_blank">http://code.google.com/p/acpypi/</a>>/<div class="im">
<br>
<br>
I hope one of these with careful selection of the force field will<br>
be helpful to you.<br>
<br>
<br>
Sincerely,<br>
-- Bruce D. Ray, Ph.D.<br>
Associate Scientist<br>
IUPUI<br>
Physics Dept.<br>
402 N. Blackford St.<br>
Indianapolis, IN 46202-3273<br>
<br>
<br>
<br>
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<br><div class="im">
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
========================================<br>
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