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 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> wrote: > On Fri, Jul 31, 2009 at 5:19:19 PM, Nancy <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 > 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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