[gmx-users] Carbohydrate MD Simulation

Nancy nancy5villa at gmail.com
Sun Aug 2 00:03:49 CEST 2009


I downloaded "topolbuild1_2_1.tgz" from the URL:

However, when I tried to decompress the file, I received the following error

# 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


but that did not work either.  Please advise.

Thank you.

On Sat, Aug 1, 2009 at 11:31 AM, Bruce D. Ray <brucedray at yahoo.com> wrote:

> On Fri, Jul 31, 2009 at 5:19:19 PM, Nancy <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
> Physics Dept.
> 402 N. Blackford St.
> Indianapolis, IN 46202-3273
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