amin-sagar

I am also trying to do this. I tried using interchange with the following script. ``` import os import torch import espaloma as esp from openff.toolkit.topology import Molecule from openmm.app...

I am also running into the same error. My script is as follows ``` modeller = Modeller(openmm_topology, openmm_positions) modeller.addSolvent(forcefield, model='tip3p', padding=1*nanometer,boxShape='octahedron',ionicStrength=0.15*molar) system = forcefield.createSystem(modeller.topology, nonbondedMethod=PME,nonbondedCutoff=1.0*nanometer, constraints=HBonds,hydrogenMass=4*amu) temperature = 310 *...

I think I understand what was wrong. The test system is not periodic so the box vectors were not needed. For periodic systems, ``` simulation.create(thermodynamic_states=thermodynamic_states, sampler_states=[states.SamplerState(positions,box_vectors=system.getDefaultPeriodicBoxVectors())], storage=reporter) ``` this seems...

Thanks @peastman Sorry, if this is obvious, could you please point me to some scripts to save xml files in a format similar to amber99sbildn.xml after generating parameters with openff?...

Thanks @peastman At the step of structure preparation the choice of force field is not important. If I use openff instead of Espaloma, can you give me some hints about...

@victorconan @sokrypton Have you found a solution to this. I am also experiencing the same issue. Is there supposed to be a maximum number of soft iterations. My i_ptm, pLDDT...

@sokrypton Sorry, I should have mentioned. I am using design_pssm_semigreedy() protocol. The script is from #107 ``` from colabdesign.af.alphafold.common import residue_constants bias = np.zeros((af_model._binder_len,17)) # force some positions to be...

@sokrypton @victorconan This seems like a nice explanation in some cases. In the particular case that I am working on, there are multiple peptides of the same length known to...

I think a relatively simple MC position move algorithm would also be very useful. I was looking for something like that when I found this. For example, in the case...

Thanks @0merle0 That would be very helpful. I am certainly interested in implementing this. Please let me know how we can connect.