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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