[gmx-users] Structure of the input

[Justin A. Lemkul]

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.

http://manual.gromacs.org/online/pdb.html

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):

http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field
http://www.gromacs.org/Documentation/How-tos/Parameterization

-Justin

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

-- 
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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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