GROMACS version: 2021.3
GROMACS modification: No
Dears,
I am trying to simulate the diffusion of a small drug molecule across a lipid membrane.
The lipid membrane system was generated using CHARMM GUI. The input files provided by C-GUI were solvated in water and a NaCl concentration of 0.15 at a temperature of 310K. The membrane system was then minimized, equilibrated and produced using gromacs for 200ns.
In parallel, the input file for the small drug molecule was downloaded from RSCB PDB. Using avogadro, charmm-readable files of the drug were produced. Then CGenFF was used to to produce the topology.
To merge the two systems, gmx insert-molcules command was used as follows:
gmx insert-molecules -f prod.gro -ci md.gro -n index.ndx -o mem+drug.gro -replace -nmol 1 -seed 77
where:
prod.gro is the equilibrated membrane system
md.gro is the equilibrate small drug molecule
index.ndx is the index file of the membrane system (used to specify that the drug molecule will be added to the solvent NOT the membrane)
mem+drug.gro is the new merged system
Following this step, the topology was updated to include the drug molecule as follows:
#include “dm21.itp” which is the .itp file for the drug was added after the forcefiled.itp
#include “dm21.top” which is the topology file for the drug was added before the water.itp
Moreover, a new index file was generated to include the drug molecule in the SOLV index, making me have 2 index groups:
MEMB which contains all phospholipid groups & SOLV which contains Na+ ions, Cl- ions, water and the drug molecule.
While trying to minimize the system, I get the following error:
Atomtype CG2R61 not found
NB. This is the drug’s atomtype.
How do you think I can overcome this problem?
Thank you very much!