ValueError: Illegal value for nonbonded method about ommprotocol HOT 4 CLOSED

Solved it!

Thank you for your help!

from ommprotocol.

Hi!

This error is saying that the nonbonded method you chose (available options here) is not compatible with the system you specified. This can happen for example if you try to use PME, which requires periodic boundary conditions, with a system with no periodic boundary conditions. There's a change your prmtop/inpcrd does not specify the box vectors or something similar that has to do with the system preparation routines in AmberTools.

Feel free to attach the yaml, prmtop and inpcrd files in a zipped folder and I will take look.

from ommprotocol.

Thank you for your quick response!
Please find attached the requested files.

md.zip

from ommprotocol.

In [1]: import parmed as pmd

In [2]: top = pmd.load_file("/home/jaime/win/Downloads/md/step5assembly_tleap.prmtop")

In [3]: top.box
# empty

In [5]: crd = pmd.load_file("/home/jaime/win/Downloads/md/step5assembly_tleap.inpcrd")

In [6]: crd.box
#empty 

Your files do not define box vectors, but you are using nonbondedMethod: PME, which requires them. If you change it to nonbondedMethod: CutoffNonPeriodic it will work, but I don't think you want to run this system without periodic boundary conditions.

While preparing your prmtop and inpcrd in tleap/xleap, make sure to enable this option. Check the Amber tutorials for more info.

Also, if you have computed the box vectors via other means, you can still pass them to ommprotocol via the box_vectors key:

# input
topology: step5assembly_tleap.prmtop
positions: step5assembly_tleap.inpcrd
box_vectors: some_custom_vectors.csv

The simplest option might be a .csv file. Check here for details.

from ommprotocol.