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



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--
========================================

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

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