[gmx-users] Protein-Ligand Interaction calculation

[Justin Lemkul]

On 2/17/20 7:18 AM, Peter Mawanga wrote:
> Hello everyone
>
> I used the CHARMM-GUI Membrane Builder to build a bilayer around my
> protein-ligand complex.
>
> However, unfortunately the ligand was not mentioned separately in the index
> (.ndx) file although it was mentioned in the topology (.top) file. Hence I
> am not able to calculate the energy between the protein and ligand using
> the energy (.edr) file.
>
> Please let me know if there is any workaround for this. It would be
> difficult to repeat the simulations again.
>
>

Computing interaction energy is a post-processing task. You should not 
specify energygrps in your .mdp file for the actual simulation because 
(1) it slows the simulation down and (2) it's not compatible with GPUs.

All you need to do is generate a new .tpr file with the desired 
energygrps (you don't even need a special index file because all 
non-standard [moleculetype] entries are by default assigned to their own 
index groups) and use mdrun -rerun on the existing trajectory and the 
new .tpr file with energygrps.

-Justin

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Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
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Virginia Tech Department of Biochemistry
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jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

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