[gmx-users] Carbohydrate MD Simulation

[Justin A. Lemkul]

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

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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