inniag / openmm-scripts-amoeba Goto Github PK

In the origin opemm, the amoeba force field only provides the parameters for stardard amino acid residues.
So can the python script tinker2opennmm.py used to generate amoeba force field of nonstandrard amino acid residue?

Hello,

Thanks for sharing your AMOEBA OpenMM scripts! I have a question regarding how you are calculating your dipole moment profile - it seems that you are using the center of geometry of the water molecules to calculate the monopole charge weighted positions from, is this correct? Then you are binning the vector sum of the monopole charge weighted positions, lab frame permanent dipoles and induced dipoles on the center of geometry?

Unfortunately I cannot seem to reproduce the z component of the dipole moment of the AMOEBA14 water model if I use the center of geometry to calculate my monopole charge weighted positions term...

I asked a similar question on the OpenMM github page (openmm/openmm#3141), and it was suggested that the correct reference point to use instead would be the center of mass.

I know the dipole moment profiles probably don't change all that much but I am finding that it does become important for example in studying the z component of the dipole moment of nanoconfined water molecules right at an interface.

Thanks for reading!

Hello,

First of all I'd like to thank you for creating the AMOEBA force field files for the POPE lipids. I have been trying to run a pure POPE bilayer system using the scripts available here. I am facing issues with creating the simulations as simulate_amoeba crashes while guessing the bonds for the POPE lipids.

I have obtained the initial structure for a 72 lipid POPE bilayer system from CHARMM-GUI. When I run the simulate_amoeba on this pdb file, I receive the error

ValueError: No template found for residue 5 (POPE). The set of atoms matches POPE, but the bonds are different.

I have checked the residue 5, nothing seems to be wrong about it. It has the same atoms with the same order as the others. I add the Google Drive link to the file if anyone would like to take a look at it

What could be going on here? Also, is there any alternative ways to create a pure bilayer simulation with OpenMM using the AMOEBA force field?

Thank you.