[gmx-users] Re: gromacs question topologie

Justin A. Lemkul jalemkul at vt.edu
Mon Aug 29 14:49:18 CEST 2011

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.


> 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
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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