diff --git a/_posts/2023-11-8-Peptide-Docking-with-ADCP-2.md b/_posts/2023-11-8-Peptide-Docking-with-ADCP-2.md index 8d25617d3d..81aaa51b81 100644 --- a/_posts/2023-11-8-Peptide-Docking-with-ADCP-2.md +++ b/_posts/2023-11-8-Peptide-Docking-with-ADCP-2.md @@ -36,7 +36,7 @@ peptide-docking/ + [Docking Calculation](#docking-calculation) * [Example 1-2 Basic Minimization: Using OpenMM for a Two-step Minimization](#example-1-2-basic-minimization-using-openmm-for-a-two-step-minimization) + [Gas Phase Minimization](#gas-phase-minimization) - + [Minimization Preparation](#minimization-preparation) + + [2nd Minimization Preparation](#2nd-minimization-preparation) + [Minimization with Implicit Solvent](#minimization-with-implicit-solvent) * [Example 2-1 Interfacing RDKit: Exporting ADCP raw outputs into RDKit Molecules and Using Vina for Local Optimization] @@ -128,9 +128,9 @@ However, it should be noted that **not all poses can be properly minimized withi In the 100 processed modes, that seemed to be the only problematic structure that remained unphysical after the 100-step minimization in vacuo. -The above minimization calculation (-nmin 100 -nitr 100) will take **about 1 hour** on a 40-core Intel(R) Xeon(R) Gold 6148 CPU @ 2.40GH. The completed minimization calculation will generate `dock1_omm_rescored_out.pdb` under the work folder `dock1`. With the `-k` option, subfolder `dock1_omm_amber_parm` will be kept under `dock1`. +The above minimization calculation (-nmin 100 -nitr 100 -env vaccum) will take **about 1 hour** on a 40-core Intel(R) Xeon(R) Gold 6148 CPU @ 2.40GH. The completed minimization calculation will generate `dock1_omm_rescored_out.pdb` under the work folder `dock1`. With the `-k` option, subfolder `dock1_omm_amber_parm` will be kept under `dock1`. -### Minimization Preparation +### 2nd Minimization Preparation To start another minimization, I will do the following 3 things: @@ -250,7 +250,9 @@ In which I set `-nitr` to be 1000. See below for the energy outputs I collected | 2000 | -4896.49 | -4669.85 | -193.37 | -33.27 | -226.64 | | 5000 | -4883.27 | -4657.35 | -191.20 | -34.72 | -225.92 | -You will see that the energies, most importantly `dE_Interaction`, became generally invariant after `-nitr` reached 1000. But again we should keep in mind that the required number of minimization steps always depends on how good the initial structure is... +You will see that the energies, most importantly `dE_Interaction`, became generally invariant after `-nitr` reached 1000. But again we should keep in mind that the required number of minimization steps always depends on how good the initial structure is... + +The above minimization calculation (-nmin 100 -nitr 1000 -env implicit) will take ??? on a 40-core Intel(R) Xeon(R) Gold 6148 CPU @ 2.40GH. ## Example 3 Advanced Docking: Docking a Cyclice Peptide Containing a Disulfide Bond and Pose Selection