How to use mdanalysis to deal with non-standard amino acid systems

[ldx022]

Hello everyone!
I've encountered some issues while processing my coarse-grained system with MDAnalysis. In general, my system is quite unique, not a very standard MD system, but a coarse-grained system I built manually. Overall, this system's topology files include only .top, .gro, and .psf files. However, I previously tried reading the .top format topology file with MDAnalysis and failed (I guess it might be due to non-standard amino acid names?). The .psf file seems like doesn't pair with the .xtc trajectory (although in VMD, the .xtc trajectory can load the .psf topology file for visualization, but not in MDAnalysis), so only .gro is used as the topology file. Could you please tell me MDAnalysis reads .xtc trajectories, what would be the most appropriate format for the accompanying topology file? How can MDAnalysis be used to solve problems like the ones I'm experiencing?

[hmacdope]

Hi @ldx022, you should be able to pair any topology format with any trajectory format basically, with the only constraint that the number of particles in each matches. For your use case (sounds like you used GROMACS) using a .gro and a .xtc file sounds like a good option. MDAnalysis does read .xtc files. The topology parsing from a .top GROMACS format include file is more complicated and can sometimes not work as intended .

import MDAnalysis as mda
u = mda.Universe("system.gro", "trajectory.xtc")

should work.