GROMACS version: gromacs/2024.3
GROMACS modification: No
Hello everyone,
I’m currently trying to build a monolayer/protein system in CHARMM-GUI using the CHARMM36 force field and simulate it with the OPC water model in GROMACS. However, CHARMM-GUI does not allow me to select the water model after choosing CHARMM36, and it defaults to TIP3P. I’ve tried to manually rename the water molecules in the output files to match the OPC water model, but I keep encountering errors when trying to prepare the simulation in GROMACS.
Here’s what I’ve done:
Renamed the TIP3P water molecules to OPC (e.g., TIP3 to OPC, OH2 to OW, H1 to HW1, H2 to HW2). I also tried renaming TIP3 to SOL instead of OPC and it didn’t work.
Used the formula a=b=0.5×const=0.147722363a = b = 0.5 \times \text{const} = 0.147722363a=b=0.5×const=0.147722363 for calculating the dummy site (which I named MW or I also tried naming it EPW) as I’ve seen both used in different OPC.itps available online.
Attempted to update the input files accordingly but received the following error:
Fatal error:
Something is wrong in the coordinate formatting of file modified_step5_input.gro.
Note that gro is fixed format (see the manual).
I’ve also tried modifying the PDB file to match the OPC water model, but I get similar errors when I try to process it in GROMACS.
My question is:
Is there a standard workflow for converting CHARMM-GUI outputs (with TIP3P) to the OPC water model for GROMACS simulations using the CHARMM36 force field? If manually modifying the files created by CHARMM-GUI is a viable solution, are there any potential issues I should be aware of that might arise later in the simulation process?
Any advice or suggestions would be greatly appreciated!
Why do you want to simulate this water model? There is a reason why CHARMM-GUI uses TIP3 water for CHARMM36m.
The easiest solution is to strip the system of all the water molecules and resolvate (gmx solvate) with the correct 4-sites model, and then point it to the OPC topology. Renaming in the .gro file is okay as long as you respect the spacing and you point to the correct topology, but adding by hand the fourth site is way more complicated than simply re-solvating.
Hi, I want to use OPC as the water model with the CHARMM36 as the literature suggests this is the optimal combination accurate description of lipid behavior at the water–air interface. Would removing the water molecules and resolvating cause an issue with the Monolayer Builder system set up from CHARMM GUI as this creates 2 monolayers separated by a water slab? I included a screenshot of how CHARMM GUI builds the system. If I resolvated, would there be a way to ensure the waters are only added between the 2 monolayers like how it is built in CHARMM GUI?
Yes, there are several ways to achieve that. The easiest is probably to just strip the system from the TIP3 water, solvate the whole system again (so also the ‘air’ interface on the top and bottom of the system), and then remove the water molecules inside the lipids and in the air volumes by creating a group with gmx select containing all the water molecules that have a z position > than the bottom leaflet lipid heads positions and < than the top leaflet lipid heads positions.
Hi, thank you so much. I’ve tried this, but I first needed to create a .gro with water in OPC format (which I haven’t been able to find available online) so I made a .gro of a single OPC water molecule by using tleap in amber to get a pdb of a water box in OPC then converting it to gro format. Is there a better way to do this?
With my OPC.gro containing 1 OPC water molecule, I tried to run: gmx_mpi solvate
This correctly added waters to the entire system (including the ‘air’ interface on the top and bottom) but it is not nearly enough waters. I’ve tried specifying the box dimensions to be larger to get more waters to be included but this hasn’t worked.
If I know I need ~13755 waters to end up in between the monolayers, is there a way to specify this when trying to solvate my system?
First, the specific water model is defined by the topology you are using rather than the .gro file. This means that the most important part is using a four-points water model to solvate the system (as OPC is four-points). You can do this by specifying the flag -cs tip4p.gro in the solvate command. You then have to check that the atom names and numbering reported in your OPC topology (the .itp file) is consistent with what GROMACS added.
I would retry with this new flag and see if you get enough water everywhere. Then you will need to remove the water from where you do not need it (which will be a combination of gmx select and gmx trjconv most likely).
