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">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>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/">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 class="gmail_quote">On Sat, Aug 1, 2009 at 11:31 AM, Bruce D. Ray <span dir="ltr"><<a href="mailto:brucedray@yahoo.com">brucedray@yahoo.com</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><div style="font-family: times new roman,new york,times,serif; font-size: 10pt;"><div class="im">
<span style="font-family: times new roman,new york,times,serif;">On Fri, Jul 31, 2009 at </span><font style="font-family: times new roman,new york,times,serif;" face="Tahoma" size="2">5:19:19 PM, </font><font style="font-family: times new roman,new york,times,serif;" face="Tahoma" size="2">Nancy <<a href="mailto:nancy5villa@gmail.com" target="_blank">nancy5villa@gmail.com</a>> wrote:</font><br>
> If it necessary to manually create force field parameters for each
molecule, then how can one run a<br>> simulation involving a number of
arbitrary molecules (e.g. a set 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
running simulations on<br>> arbitrary molecules without having to "piece
together" a force field for each molecule?<br><br></div>Provided that the desired force field has suitable parameters for a particular bonding situation<br>already, there are software packages that can generate a potentially suitable topology from<br>
a molecule's structure. For gromacs topologies, user contributions to gromacs include<br>topolbuild 1.2.1 that supports amber, gaff, glycam, Tripos, and gromacs force fields<br>(my upcoming version 1.3 will also do OPLS-AA with the numeric opls atom types), and<br>
topolgen 1.1, a Perl script that supports OPLS-AA. Also available in user contributions<br>is ambconv that takes the file generated by antechamber and leap from amber tools<br>and generates a gromacs topology that uses the amber or gaff forcefield selected when<br>
leap was applied to the antechamber output. Another option is the Perl script<br><span>mktop at <<a href="http://labmm.iq.ufrj.br/mktop/" target="_blank">http://labmm.iq.ufrj.br/mktop/</a>>, documented in Ribeiro, A.A.S.T., Horta, B.A.C.,</span><br>
and de Alencastro, R.B. J. Braz. Chem. Soc., Vol. 19, No. 7, 1433-1435, 2008. Also<br>there is acpypi, the AnteChamber Python Parser Interface available at<br><span><<a href="http://code.google.com/p/acpypi/" target="_blank">http://code.google.com/p/acpypi/</a>>.</span><i><a href="http://code.google.com/p/acpypi/" style="text-decoration: none;" target="_blank"></a></i><div style="color: black; background-color: transparent;">
</div><br>I hope one of these with careful selection of the force field will be helpful to you.<br><br><br>Sincerely,<br><div> </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<br><br></div><br>
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