Please keep all Gromacs-related correspondence on the gmx-users list,
particularly if the discussion was previously carried out there. I am not a
private tutor.
Joschua Sterzenbach wrote:
Hi
is in the coordinate file only the geometry of the molecule?
Yes. Have a look at its contents - all you'll find in most common formats are
the (x,y,z) coordinates of the named atoms.
I ask because I only have the geometry.
Do I get the topologie out of the geometry or from where comes it?
Please do some basic tutorial material to understand the Gromacs workflow. For
residue-based biomolecules like proteins and nucleic acids, use pdb2gmx. For
other molecules, g_x2top can create basic topologies for a limited number of
force fields and molecules. Otherwise, you'll have to obtain the topology by
some other means. There are other programs on the User Contributions page of
the Gromacs site that can produce topologies for arbitrary molecules.
You haven't said yet what you're working with, so all I can do is venture
guesses.
-Justin
The questions corresponds to this:
http://www.mail-archive.com/gmx-users@gromacs.org/msg43478.html
Thanks
Regards
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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