Hi users,
I have a doubt regarding the simulation of small molecule in bilayer system. The bilayer system is generated using charmm gui. The small molecule need to be placed in water, on the surface of bilayer.
The ligand is polyene structure.
Is there any method by which I can insert the molecule into the system.
The insert molecule command doesn’t work du to the absence of solvation box. So I tried creating a solvation box using “gmx editconf -f ligand.pdb -ci lipid.gro -o output.gro -bt cubic -d 1.0”
But the insert molecule command ends up with error, undefined solute box. I tried adding the solute box explicitly using -box flag to editconf, but the error prevails.
Any suggestions on how to perform this simulation?
Hi,
did you try gmx insert-molecules gmx insert-molecules — GROMACS 2020.5 documentation with the option -ip?
Best regards
Alessandra
Hi.
Thanks for the reply.
Insert molecule was more complicated for me. The I used charmm gui which was able to generate the complex system.