[gmx-users] [gmx-developers] How to get IEM of a protein
jalemkul at vt.edu
Tue Jun 26 01:55:32 CEST 2018
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On 6/25/18 7:51 PM, Gideon Smith wrote:
> 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.
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu | (540) 231-3129
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