Removing ring penetrations and chirality errors

In this page, we explain how to remove ring penetrations and chirality errors in a protein using GENESIS. Here, we use spdyn. The same scheme is available in atdyn. The scheme in the below figure will be performed 1. For details, please read the GENESIS user manual ([MINIMIZE] chapter).

Preparation

All the files required for this tutorial are hosted in the GENESIS tutorials repository on GitHub.

If you haven’t downloaded the files yet, open your terminal and run the following command (see more in Tutorial 1.1):

$ cd ~/GENESIS_Tutorials-2022

# if not yet
$ git clone https://github.com/genesis-release-r-ccs/genesis_tutorial_materials

If you already have the tutorial materials, let’s go to our working directory:

$ cd genesis_tutorial_materials/tutorial-A.6

This tutorial is mainly composed of two steps: (1) system setup and (2) energy minimization. The energy minimization is further composed of three steps to remove ring penetrations and chirality errors. Control files for GENESIS are already included in the tutorial folder. Since we use the CHARMM36m force field parameters, we make a symbolic link to the CHARMM toppar directory (see Tutorial 2.2).

# Check the contents in Appendix 6
$ ln -s ../../Data/Parameters/toppar_c36_jul21 ./toppar
$ ln -s ../../Programs/genesis-2.0.0/bin ./bin
$ ls 
INP1  INP2  INP3  bin  setup  toppar

# Setup the initial PDB and PSF files
$ cd setup
$ ls
build.tcl  proa.pdb

$ vmd -e build.tcl
$ ls
build.tcl    ionized.psf  protein.pdb  wbox.log  wbox.psf
ionized.pdb  proa.pdb     protein.psf  wbox.pdb

$ cd ../

Energy minimization

Step1: Run basic minimization

First, we carry out a basic energy minimization for this system.

# Check the control file
$ less INP1

[MINIMIZE] 
method        = SD     # [SD]
nsteps        = 5000   # number of minimization steps
crdout_period = 1000
rstout_period = 5000

# Run minimization
$ export OMP_NUM_THREADS=4
$ mpirun -np 8 ./bin/spdyn INP1 > log1
$ ls
INP1  INP2  INP3  log1  min1.dcd  min1.rst  bin  setup  toppar

$ less log1

However, in the log message you can see that there are several residues that may have ring penetrations or chirality errors in the energy minimized structure.

Check_Ring_Structure> Check ring structure

  suspicious ring group id = 12 : TRP 68 (atom = 1011) max_bond_length = 1.921

  WARNING!
  Some suspicious residues were detected. Minimization might be too short, or "ring penetration"
  might happen in the above residues. Check the structure of those residues very carefully.
  If you found a ring penetration, try to perform an energy minimization again 
  with the options "check_structure = YES" and "fix_ring_error = YES" in [MINIMIZE].
  The energy minimization should be restarted from the restart file obtained in "this" run.
  For more information, see the chapter on [MINIMIZE] in the user manual.

Check_Chirality> Check chirality

  suspicious chiral group id = 5  : GLU 5  (atom = 62)  angle = 178.549
  suspicious chiral group id = 32 : PRO 32 (atom = 488) angle = 85.871

  WARNING!
  Some suspicious residues were detected. Minimization might be too short, or "chirality error"
  might happen in the above residues. Check the structure of those residues very carefully.
  If you found a chirality error, try to perform an energy minimization again
  with the options "check_structure = YES" and "fix_chirality_error = YES" in [MINIMIZE].
  The energy minimization should be restarted from the restart file obtained in "this" run.
  For more information, see the chapter on [MINIMIZE] in the user manual.

Let’s check the corresponding residues carefully using a molecular viewer software.

Step2: Run minimization to remove errors

In order to remove the ring penetrations and chirality errors, we restart the energy minimization using min1.rst. Let’s take a look at INP2. In the [MINIMIZE] section, fix_ring_error and fix_chirality_error options are added. Basically, these options should be added only when the error was found in the energy minimized structure.

[INPUT] 
topfile = ./toppar/top_all36_prot.rtf
parfile = ./toppar/par_all36m_prot.prm
strfile = ./toppar/toppar_water_ions.str
psffile = ./setup/ionized.psf
pdbfile = ./setup/ionized.pdb
rstfile = min1.rst

[MINIMIZE] 
method              = SD    # [SD]
nsteps              = 5000  # number of minimization steps
crdout_period       = 1000
rstout_period       = 5000
fix_ring_error      = YES
fix_chirality_error = YES

Run the energy minimization again using INP2.

# Run minimization
$ mpirun -np 8 ./bin/spdyn INP2 > log2
$ less log2

However, unfortunately, we could not fix the chirality error in Pro32 in this run.

Check_Ring_Structure> Check ring structure

  No suspicious residue was detected.

Check_Chirality> Check chirality

  suspicious chiral group id = 32 : PRO 32 (atom = 488) angle = 171.247

  WARNING!
  Some suspicious residues were detected. Minimization might be too short, or "chirality error"
  might happen in the above residues. Check the structure of those residues very carefully.
  If you found a chirality error, try to perform an energy minimization again
  with the options "check_structure = YES" and "fix_chirality_error = YES" in [MINIMIZE].
  The energy minimization should be restarted from the restart file obtained in "this" run.
  For more information, see the chapter on [MINIMIZE] in the user manual.

Step3: Second trial to remove the remaining errors

So, we run the energy minimization again using INP3, in which fix_chirality_error = YES is specified.

[INPUT] 
topfile = ./toppar/top_all36_prot.rtf
parfile = ./toppar/par_all36m_prot.prm
strfile = ./toppar/toppar_water_ions.str
psffile = ./setup/ionized.psf
pdbfile = ./setup/ionized.pdb
rstfile = min2.rst

[MINIMIZE]  
method              = SD    # [SD]
nsteps              = 5000  # number of minimization steps
crdout_period       = 1000
rstout_period       = 5000
fix_chirality_error = YES

# Run minimization
$ mpirun -np 8 ./bin/spdyn INP3 > log3
$ less log3

Now, you can see that there are no suspicious residues. Please take a look at Trp68, Glu5, and Pro32 to check whether the errors were actually removed. Then, you can use the obtained restart file (min3.rst) for the subsequent MD simulation.

Check_Ring_Structure> Check ring structure

  No suspicious residue was detected.

Check_Chirality> Check chirality

  No suspicious residue was detected.

Written by Takaharu Mori@RIKEN Theoretical molecular science laboratory, June 2022

References

  1. Mori T., Terashi G., Matsuoka D., Kihara D., Sugita Y., 2021, J. Chem. Inf. Model., 61, 3516–3528. ↩

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