GROMACS version: 5.1.4
GROMACS modification: No
Here post your question
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.
Gromacs version: 2021.4
As a new gromacs user, I am trying to simulate neoxanthin and since it’s not a commonly simulated molecule, I asked the researchers involved for the needed files. I got the parameters for it in the form of .itp file. I am confused about how to use this file and incorporate its information so that I can use gromacs to simulate it without any errors. I used the “-i” flag option in pdb2gmx to include my .itp file but I still get this error. Searching through the gromacs common errors link, I found this:
“find a topology file for the molecule, convert it to an itp file and include it in your top file”
But my question is that the top file is one of the files I am trying to make using the pdb2gmx so how can I include the .itp file in it?
I would really appreciate any help, Thank you so much.
How would we add monoatomic molecules such as the noble gases to the GROMACS force fields (the AMBER99SB-ILDN ff, say). I would like to introduce noble gases to the simulation box, alongside conventional DNA and protein chains and simulate them. I tried to obtain the topology for a Kr atom (coordinates saved from a PDB file containing protein and Kr atoms) from the server ACPYPE, which provides GROMACS-compatible .itp topology files for uploaded coordinates of non-standard molecules. However, it said that it found an unrecognised atom type. Please help.