Body: <p>Is this possible to generate force fields for any residue in my .pdb file? I am trying to generate conformations for the proteins with arbitrary residues binded to it from .pdb files using OpenMM, but there are always errors like 'missing residue VAL, missing residue HEM, etc'. I tried to use pdbfixer from openmm library, skip\replace missing\nonstandard residues using GROMACS and generate .top .gro, but even after that it shows me errors or generates nonsence if I replace residues. I read some articles and looks like generating force fields is a complicated task. But still wondering is there any open-source framework\library\neural network that can generate such force fields?</p>
  <p>For example I follow this guide</p>
  <p><a href="http://docs.openmm.org/latest/userguide/application/02_running_sims.html#a-first-example" rel="nofollow noreferrer">http://docs.openmm.org/latest/userguide/application/02_running_sims.html#a-first-example</a></p>
  <p>Whenever I try to run the following code</p>
  <pre><code>from openmm.app import *
  from openmm import *
  from openmm.unit import *
  from sys import stdout
  
  pdb = PDBFile('input.pdb')
  forcefield = ForceField('amber14-all.xml', 'amber14/tip3pfb.xml')
  system = forcefield.createSystem(pdb.topology, nonbondedMethod=PME,
          nonbondedCutoff=1*nanometer, constraints=HBonds)
  integrator = LangevinMiddleIntegrator(300*kelvin, 1/picosecond, 0.004*picoseconds)
  simulation = Simulation(pdb.topology, system, integrator)
  simulation.context.setPositions(pdb.positions)
  simulation.minimizeEnergy()
  simulation.reporters.append(PDBReporter('output.pdb', 1000))
  simulation.reporters.append(StateDataReporter(stdout, 1000, step=True,
          potentialEnergy=True, temperature=True))
  simulation.step(10000)
  </code></pre>
  <p>It shows</p>
  <pre><code>No template found for residue (number) (residue_name)
  </code></pre>
  <p>for every .pdb file that I am trying to run and every ForceField parameter permutation.
  As an example I tried to run simulations on this protein
  <a href="https://www.rcsb.org/structure/1a3n" rel="nofollow noreferrer">https://www.rcsb.org/structure/1a3n</a></p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-11-27T01:14:45.090Z
Comments.Text: Please clarify your specific problem or provide additional details to highlight exactly what you need. As it's currently written, it's hard to tell exactly what you're asking.
Comments.UserDisplayName: Community
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-11-27T14:13:31.267Z
Comments.Text: when you say "force field", can you be more specific? it seems like a force field is a step in your workflow rather than your goal. "generate conformations for the proteins with arbitrary residues binded to it": what does this mean? What exactly are you modeling?  what exactly are you doing to your pdb file? can you give examples?
Comments.UserDisplayName: Maximilian Press
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-11-28T05:53:20.020Z
Comments.Text: Do you mean "electron density clouds"?
Comments.UserDisplayName: gringer
Tags: <proteins>
Title: Generating force-fields for ANY residue
ThreadText: # Generating force-fields for ANY residue
  
  (Asked by: username_0 on 2023-11-26)
  
  Is this possible to generate force fields for any residue in my .pdb file? I am trying to generate conformations for the proteins with arbitrary residues binded to it from .pdb files using OpenMM, but there are always errors like 'missing residue VAL, missing residue HEM, etc'. I tried to use pdbfixer from openmm library, skip\replace missing\nonstandard residues using GROMACS and generate .top .gro, but even after that it shows me errors or generates nonsence if I replace residues. I read some articles and looks like generating force fields is a complicated task. But still wondering is there any open-source framework\library\neural network that can generate such force fields?
  
  For example I follow this guide
  
  <http://docs.openmm.org/latest/userguide/application/02_running_sims.html#a-first-example>
  
  Whenever I try to run the following code
  
  ```
  from openmm.app import *
  from openmm import *
  from openmm.unit import *
  from sys import stdout
  
  pdb = PDBFile('input.pdb')
  forcefield = ForceField('amber14-all.xml', 'amber14/tip3pfb.xml')
  system = forcefield.createSystem(pdb.topology, nonbondedMethod=PME,
          nonbondedCutoff=1*nanometer, constraints=HBonds)
  integrator = LangevinMiddleIntegrator(300*kelvin, 1/picosecond, 0.004*picoseconds)
  simulation = Simulation(pdb.topology, system, integrator)
  simulation.context.setPositions(pdb.positions)
  simulation.minimizeEnergy()
  simulation.reporters.append(PDBReporter('output.pdb', 1000))
  simulation.reporters.append(StateDataReporter(stdout, 1000, step=True,
          potentialEnergy=True, temperature=True))
  simulation.step(10000)
  
  ```
  
  It shows
  
  ```
  No template found for residue (number) (residue_name)
  
  ```
  
  for every .pdb file that I am trying to run and every ForceField parameter permutation.
  As an example I tried to run simulations on this protein
  <https://www.rcsb.org/structure/1a3n>
  
  **Tags:** proteins
  
  > **Comments:**
  > **username_1**: Please clarify your specific problem or provide additional details to highlight exactly what you need. As it's currently written, it's hard to tell exactly what you're asking.  
  > **username_2**: when you say "force field", can you be more specific? it seems like a force field is a step in your workflow rather than your goal. "generate conformations for the proteins with arbitrary residues binded to it": what does this mean? What exactly are you modeling?  what exactly are you doing to your pdb file? can you give examples?  
  > **username_3**: Do you mean "electron density clouds"?  
  
  ---
  
  ## 0 answers
  
  