GROMACS version: 5.1.4
GROMACS modification: No
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Hello, I am an undergraduate student who are studying GROMACS.
I tried to simulate for I2 molecule in water solvent, but I have some problems running the program.
When I tired to do pdb2gmx, it says that ‘Residue not found in residue topology database.’
So, I tried to make .gmx extension directly, but there are several problems with topol.top.
I require the advice to solve this problem or the appropriate .pdb format.
I know that it is very basic and elementary problem, but I have no one to require helps.
Sorry for asking such a ridiculous question.
Thank you.
In the case that the forcefield doesn’t have the residue in its database, you basically have to generate your own topology (.itp file). A list of different servers that do this for you can be found here (Protein-Ligand Complex), ATB specifically already has the .itp and .pdb files generated for molecular Iodine if you search it up.
Since pdb2gmx only works if the residue exists in the forcefield, you’ll have to make your own topol.top file, which would include the #include command to call whichever forcefield you’re using and the data from the .itp file (an example of making your own .top file for CO2 and using it to run simulations can be found at http://www.mdtutorials.com/gmx/vsites/02_topology.html). Once you have the .pdb and .top files, you can continue as you would with this first tutorial (Lysozyme in Water).
Please don’t worry about whether the question is ridiculous, feel free to ask any follow-ups.