[gmx-developers] How to get IEM of a protein

Justin Lemkul jalemkul at vt.edu
Tue Jun 26 01:55:32 CEST 2018

The developers list is for discussions related to code and GROMACS 
development. I am CCing your message over to the gmx-users mailing list, 
which is for general GROMACS questions and discussion.

On 6/25/18 7:51 PM, Gideon Smith wrote:
> Hi
> I am new to gromacs, and I need to calculate the Interaction Energy 
> Matrix of a protein, which uses g_enemat command, but that requires 
> for me to input .edr , .dat file.
> Now I only have a pdb file to input, from that i can generate .gro 
> file and I dont know how to generate .edr and .dat file.
> Also I do not need to simulate any protein, it is just that I want the 
> energy (LJ + coulombic) from the pdb file in form of IEM.

Start with some basic tutorial material. To get what you want, you need 
to generate a topology, making use of some existing functional form and 
associated parameters (which is the way to get energies) and compute the 
energy with mdrun -rerun on your configuration. All of this still 
requires you to understand how to generate that topology and assemble a 
sensible .tpr file.



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


More information about the gromacs.org_gmx-developers mailing list