GROMACS version: 2023.1
GROMACS modification: Yes/No
Hello.
I am new student of MD simulation and I started by learning 1aki (Lysozyme in water) simulation tutorial. Now I was given assignment of performing simulation of small molecules eg 90 molecules of 1-propanol in 10 water molecules. Here is how I plan to conduct the work:
I used Gaussian program to obtained the pdb files of the molecules then I used Ligpargen server to obtain the .itp and .gro files. I employed packmol to pack the molecules in one pdb file then converted it to .gro by openBabel. I intend to use md, nvt, em.mdp files of 1aki simulation tutorial in the work but I have no idea on how to get topol.top file of my system.
All the ideas that I saw and adopted the Gromacs program return one error or the other, in the energy minimization step. Below are the files the command and the error message of the stage I was now.
The command
gmx grompp -f em.mdp -c 1ppnaqbox.gro -p topol.top -o em.tpr
The Error Message
ERROR 1 [file topol.top, line 15]:
Atomtype CH3 not found
The Files
em.mdp (1.0 KB)
topol.top (720 Bytes)
1ppnaqbox.gro failed to be uploaded