# Performing Simulation for Begginer

**URL:** <https://gromacs.bioexcel.eu/t/performing-simulation-for-begginer/6673>\
**Category:** User discussions\
**Created:** [June 23, 2023, 5:02am UTC](https://gromacs.bioexcel.eu/t/performing-simulation-for-begginer/6673 "2023-06-23T05:02:22Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![umar](https://avatars.discourse-cdn.com/v4/letter/u/59ef9b/32.png) [@umar](https://gromacs.bioexcel.eu/u/umar)\
**Post date:** [June 23, 2023, 5:02am UTC](https://gromacs.bioexcel.eu/t/performing-simulation-for-begginer/6673/1 "2023-06-23T05:02:22Z")

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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](https://gromacs.bioexcel.eu/uploads/short-url/V1V3vdr3w5cwghcTpXzj8CTSdZ.mdp) (1.0 KB)  
[topol.top](https://gromacs.bioexcel.eu/uploads/short-url/aD9fUQ4VNpFEr8aTC47820qfsNq.top) (720 Bytes)  
1ppnaqbox.gro failed to be uploaded

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<div class="post-metadata">

**Author:** ![Teslim](https://avatars.discourse-cdn.com/v4/letter/t/f1d935/32.png) [@Teslim](https://gromacs.bioexcel.eu/u/Teslim)\
**Post date:** [June 23, 2023, 4:23pm UTC](https://gromacs.bioexcel.eu/t/performing-simulation-for-begginer/6673/2 "2023-06-23T16:23:56Z")

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Yes, you are not using the right atomtype. I will advise that you check the ffnonbonded.itp of the oplsaa ff. Generally, the atom types has forms oplsa123…you can try using tools like [acpype](https://bmcresnotes.biomedcentral.com/articles/10.1186/1756-0500-5-367) to generate a sample itp/top file.

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<div class="post-metadata">

**Author:** ![umar](https://avatars.discourse-cdn.com/v4/letter/u/59ef9b/32.png) [@umar](https://gromacs.bioexcel.eu/u/umar)\
**Post date:** [June 24, 2023, 6:27am UTC](https://gromacs.bioexcel.eu/t/performing-simulation-for-begginer/6673/3 "2023-06-24T06:27:54Z")

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Okay.  
Thank You.