[gmx-users] Carbohydrate MD Simulation

[Nancy]

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 <jalemkul at 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 <brucedray at yahoo.com<mailto:
>> brucedray at yahoo.com>> wrote:
>>
>>    On Fri, Jul 31, 2009 at 5:19:19 PM, Nancy <nancy5villa at gmail.com
>>    <mailto:nancy5villa at 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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>>
>>
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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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