[gmx-users] Structure of the input

Justin A. Lemkul jalemkul at vt.edu
Tue Sep 20 18:58:25 CEST 2011

Lara Bunte wrote:
> Hi
> I have a geometry in a textfile which looks like that:
> N                     2.823790   -0.041893    0.737832
> C                     3.563329   -1.141307    0.332899
> O                     4.781032   -1.165954    0.346660
> You see the atom and then three spatial coordinates. I renamed it to 
> file.pdb an give it into gromacs by pdb2gmx -f file.pdb but it did not 
> work. How I have to change this input file?

The file must adhere to correct PDB format; you can't simply rename it.


Spacing matters.  Also, if you want pdb2gmx to create a topology, you'll have to 
create an .rtp entry for it and likely an .hdb entry as well to build an intact 
molecule.  Please refer to the following resources (in addition to the manual, 
Chapter 5):



> My first aim is to do an energy minimization.
> Greetins
> Lara


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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