I used gzip to uncompress the file first: # gzip -d topolbuild1_2_1.tgz
and then I used tar: # tar -xvf topolbuild1_2_1.tar This seems to work. On Sat, Aug 1, 2009 at 6:05 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > Nancy wrote: > >> Hello, >> >> I downloaded "topolbuild1_2_1.tgz" from the URL: >> http://www.gromacs.org/@api/deki/files/40/=topolbuild1_2_1.tgz >> >> However, when I tried to decompress the file, I received the following >> error message: >> >> # tar -xvf topolbuild1_2_1.tgz >> > > You have to unzip it as well, i.e.: > > tar -zxvf topolguild1_2_1.tgz > > -Justin > > tar: This does not look like a tar archive >> tar: Skipping to next header >> tar: Archive contains obsolescent base-64 headers >> tar: Error exit delayed from previous errors >> >> I also tried to obtain topolbuild 1.2.1 from >> >> >> http://oldwww.gromacs.org/component/option,com_docman/task,doc_download/gid,111/Itemid,26/ >> >> but that did not work either. Please advise. >> >> Thank you. >> Nancy >> >> >> >> On Sat, Aug 1, 2009 at 11:31 AM, Bruce D. Ray <bruced...@yahoo.com<mailto: >> bruced...@yahoo.com>> wrote: >> >> On Fri, Jul 31, 2009 at 5:19:19 PM, Nancy <nancy5vi...@gmail.com >> <mailto:nancy5vi...@gmail.com>> wrote: >> > If it necessary to manually create force field parameters for >> each molecule, then how can one run a >> > simulation involving a number of arbitrary molecules (e.g. a set >> of mono and disaccharides) for >> > which there are no existing force fields? >> > >> > Do you know of any other MD software package that is capable of >> running simulations on >> > arbitrary molecules without having to "piece together" a force >> field for each molecule? >> >> Provided that the desired force field has suitable parameters for a >> particular bonding situation >> already, there are software packages that can generate a potentially >> suitable topology from >> a molecule's structure. For gromacs topologies, user contributions >> to gromacs include >> topolbuild 1.2.1 that supports amber, gaff, glycam, Tripos, and >> gromacs force fields >> (my upcoming version 1.3 will also do OPLS-AA with the numeric opls >> atom types), and >> topolgen 1.1, a Perl script that supports OPLS-AA. Also available >> in user contributions >> is ambconv that takes the file generated by antechamber and leap >> from amber tools >> and generates a gromacs topology that uses the amber or gaff >> forcefield selected when >> leap was applied to the antechamber output. Another option is the >> Perl script >> mktop at <http://labmm.iq.ufrj.br/mktop/>, documented in Ribeiro, >> A.A.S.T., Horta, B.A.C., >> and de Alencastro, R.B. J. Braz. Chem. Soc., Vol. 19, No. 7, >> 1433-1435, 2008. Also >> there is acpypi, the AnteChamber Python Parser Interface available at >> <http://code.google.com/p/acpypi/>./ <http://code.google.com/p/acpypi/ >> >/ >> >> I hope one of these with careful selection of the force field will >> be helpful to you. >> >> >> Sincerely, >> -- Bruce D. Ray, Ph.D. >> Associate Scientist >> IUPUI >> Physics Dept. >> 402 N. Blackford St. >> Indianapolis, IN 46202-3273 >> >> >> >> _______________________________________________ >> gmx-users mailing list gmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org> >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/search before >> posting! >> Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to gmx-users-requ...@gromacs.org >> <mailto:gmx-users-requ...@gromacs.org>. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> >> >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> gmx-users mailing list gmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/search before >> posting! >> Please don't post (un)subscribe requests to the list. Use the www >> interface or send it to gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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