# Performing Simulation for Beginner **URL:** \ **Category:** User discussions\ **Created:** [June 21, 2023, 5:16am UTC](https://gromacs.bioexcel.eu/t/performing-simulation-for-beginner/6656 "2023-06-21T05:16:58Z")\ **Posts on this page:** 9\ **Page:** 1
**Author:** ![umar](https://avatars.discourse-cdn.com/v4/letter/u/59ef9b/32.png) [@umar](https://gromacs.bioexcel.eu/u/umar)\ **Post date:** [June 21, 2023, 5:16am UTC](https://gromacs.bioexcel.eu/t/performing-simulation-for-beginner/6656/1 "2023-06-21T05:16:58Z")
Hello. I am new student of MD simulation and I started by learning 1aki 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. [nvt.mdp](https://gromacs.bioexcel.eu/uploads/short-url/c16RYacAxFJaLHM6LeLpptV4eQt.mdp) (2.1 KB) [topol.top](https://gromacs.bioexcel.eu/uploads/short-url/wtL06JYYrjmAT2LwWDZ3KHkkmUi.top) (722 Bytes) 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. PS: 1ppnaqbox.gro file do not be uploaded Thank You. ---
**Author:** ![Karis](https://avatars.discourse-cdn.com/v4/letter/k/ed8c4c/32.png) [@Karis](https://gromacs.bioexcel.eu/u/Karis)\ **Post date:** [June 25, 2023, 7:21am UTC](https://gromacs.bioexcel.eu/t/performing-simulation-for-beginner/6656/2 "2023-06-25T07:21:18Z")
This means the atomtype CH3 in the topology file is not defined in the forcefield you’re using. How did you generate the topology file to get this error? ---
**Author:** ![umar](https://avatars.discourse-cdn.com/v4/letter/u/59ef9b/32.png) [@umar](https://gromacs.bioexcel.eu/u/umar)\ **Post date:** [June 25, 2023, 10:59am UTC](https://gromacs.bioexcel.eu/t/performing-simulation-for-beginner/6656/3 "2023-06-25T10:59:51Z")
I generate the topology file by comparing with that of 1aki and also comparing with another one from simulation of small molecules through trial and error. ---
**Author:** ![Karis](https://avatars.discourse-cdn.com/v4/letter/k/ed8c4c/32.png) [@Karis](https://gromacs.bioexcel.eu/u/Karis)\ **Post date:** [June 25, 2023, 3:09pm UTC](https://gromacs.bioexcel.eu/t/performing-simulation-for-beginner/6656/4 "2023-06-25T15:09:58Z")
Have you tried using pdb2gmx ([Lysozyme in Water](http://www.mdtutorials.com/gmx/lysozyme/01_pdb2gmx.html)) to generate the topology? As long as the forcefield you choose contains that molecule’s parameters, that should output the topol.top file with the correct formatting for that forcefield ---
**Author:** ![umar](https://avatars.discourse-cdn.com/v4/letter/u/59ef9b/32.png) [@umar](https://gromacs.bioexcel.eu/u/umar)\ **Post date:** [June 26, 2023, 4:29am UTC](https://gromacs.bioexcel.eu/t/performing-simulation-for-beginner/6656/5 "2023-06-26T04:29:15Z")
Yes. I tried that and choose opls and tip3p water model but the program stated that there is no such residue in its residue topology database. ---
**Author:** ![Karis](https://avatars.discourse-cdn.com/v4/letter/k/ed8c4c/32.png) [@Karis](https://gromacs.bioexcel.eu/u/Karis)\ **Post date:** [June 26, 2023, 4:26pm UTC](https://gromacs.bioexcel.eu/t/performing-simulation-for-beginner/6656/6 "2023-06-26T16:26:29Z")
I tried checking the 1propanol.itp file in the forcefield, does it work if you try replacing the atoms section in the topol.top file with these atoms? Since you’re calling the file, it should be what the forcefield is expecting ![Screenshot 2023-06-26 at 9.24.13 AM](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/1/1320e61ad268c10162e527ce9c9b1bfe4988766d.png) ---
**Author:** ![umar](https://avatars.discourse-cdn.com/v4/letter/u/59ef9b/32.png) [@umar](https://gromacs.bioexcel.eu/u/umar)\ **Post date:** [June 27, 2023, 8:11am UTC](https://gromacs.bioexcel.eu/t/performing-simulation-for-beginner/6656/7 "2023-06-27T08:11:20Z")
I did as you suggested but see another form of error prompted ERROR 1 [file tip3p.itp, line 3]: moleculetype SOL is redefined ---
**Author:** ![Karis](https://avatars.discourse-cdn.com/v4/letter/k/ed8c4c/32.png) [@Karis](https://gromacs.bioexcel.eu/u/Karis)\ **Post date:** [July 7, 2023, 4:17am UTC](https://gromacs.bioexcel.eu/t/performing-simulation-for-beginner/6656/8 "2023-07-07T04:17:25Z")
So here’s a method that seems to work for me. Make a copy of the OPLSA forcefield folder in your working directory (you should be able to find it in gromacs/share/top/) and rename it. Put the .itp file you generated from ligpargen into that folder, then #include it in the forcefield.itp file ![Screenshot 2023-07-07 at 12.09.22 PM](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/8/8cefc81b1c98ec5f17af5df4eb3b5032aae55122.png) Use packmol to make a system of 90 propanol (I just took the .gro file grom ligpargen, used gmx editconf to convert it to .pdb, generated the system, then used gmx editconf to convert back to .gro). For the topol.top, since the molecule was already defined in the .itp file you added, you just need to include the adjusted forcefield and list out the molecules you added: ![Screenshot 2023-07-07 at 12.10.48 PM](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/c/cb399663c53e5687fffb72621c61c36b3e5a8883.png) You can then use editconf to resize the system if necessary, then use gmx solvate to add water (you can set -maxsol 10 so that only 10 water molecules are added), and it should work from this point onward. You could probably also use the 1propanol.itp that’s provided but you’d have to make sure the atoms listed in the .gro file are in the same order as those listed in the .itp file (also, the values seem different from the ligpargen files so you might need to verify which ones you want to use). Let me know if this works! ---
**Author:** ![umar](https://avatars.discourse-cdn.com/v4/letter/u/59ef9b/32.png) [@umar](https://gromacs.bioexcel.eu/u/umar)\ **Post date:** [July 9, 2023, 3:30pm UTC](https://gromacs.bioexcel.eu/t/performing-simulation-for-beginner/6656/9 "2023-07-09T15:30:47Z")
Using some manipulations, I was able to reach up to production step with -maxwarn include. But the result (from em, T, P and density plots) are not good. I will revise and adopts your contribution in the work now. Sorry for the late reply