https://github.com/vtlim/dihedral-scan

Compute dihedral scan in some molecule, such as to compare an MM force field to QM results.
https://github.com/vtlim/dihedral-scan

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Compute dihedral scan in some molecule, such as to compare an MM force field to QM results.

• Host: GitHub
• URL: https://github.com/vtlim/dihedral-scan
• Owner: vtlim
• License: gpl-3.0
• Created: 2018-12-12T21:50:37.000Z (about 6 years ago)
• Default Branch: master
• Last Pushed: 2020-01-23T01:07:25.000Z (almost 5 years ago)
• Last Synced: 2024-10-17T05:33:20.511Z (2 months ago)
• Language: Shell
• Size: 3.04 MB
• Stars: 1
• Watchers: 1
• Forks: 1
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        

# Light validation of small molecule force field

Last updated: Mar 07 2019  

This instructions list subdirectory names for each step for easier locating of relevant files.

## Contents

Brief high-level overview of contents in this repository.

```

.

├── 01_setup

│   ├── 01_setup-dihedrals.tcl

│   ├── 02_pdbPsiInput.sh

│   ├── 03_NAMDinput.sh

│   ├── minimize.inp

│   └── psfgen

│       ├── psfgen-02

│       ├── psfgen-03

│       └── psfgen.tcl

├── 02_analysis

│   ├── 01_atom-labels

│   ├── 02_parse-diheds

│   └── view_namd_scan.tcl

├── dihed_namd

│   ├── 0

│   └── 5

├── dihed_psi4

│   ├── 0

│   │   ├── dihed-0.pdb

│   │   └── mp2-631Gd

│   └── 5

│       ├── dihed-5.pdb

│       └── mp2-631Gd

├── init_namd

├── init_psi4

├── LICENSE

├── psf_from_charmm

├── README.md

└── slurm_scripts

19 directories, 65 files

```

## I. Force field generation

1. Drew structure in MarvinSketch.

    * Saved as Tripos mol2 for CGenFF.

2. [`./cgenff`] Uploaded to [CGenFF](https://cgenff.umaryland.edu/), and downloaded resulting .str file.

    * Unchecked "Guess bond orders from connectivity"

    * Unchecked "Include parameters that are already in CGenFF"

    * Unchecked "Use CGenFF legacy v1.0"

    * Edited the name after `RESI` to `GBIN` (use the resname code you want)

    * NOTE: CGenFF website summary page says current FF version is 3.0.1 but this is NOT correct according to str header and Mackerell website.

3. [`./cgenff/`] Generate PDB file for NAMD.

    * [convertExtension.py](https://github.com/vtlim/off_psi4/blob/master/tools/convertExtension.py)

    * `python convertExtension.py -i gbi-neutral-cgenff.mol2 -o gbi-neutral-cgenff.pdb`

    * Checked out the structure in VMD. Marvin did not generate a very good starting structure.

    * Edited PDB to have resname and segname of `GBIN`.

4. [`./01_setup/psfgen/`] Generate PSF file for NAMD.

    * Command: `vmd -dispdev none gbi-neutral-cgenff.pdb -e psfgen.tcl > psfgen.out`

    * NOTE: See `psf_from_charmm` directory in this repo for an alternate approach.

5. [`./02_analysis/01_atom-labels/`] Label atom numbers in VMD. Generate image to refer to later when altering atom types or choosing atoms for dihedral scan.

    * Modify displayed label at Graphics > Labels > Properties > Format to `%a::%t`

    * Did this one by one but probably could write Tcl script if larger ligand, based on `label textformat Atoms 15 { %a::%t  }`

    * Do not render as (Tachyon, Postscript) since messes up label location. Cluster super slow, so I just screenshotted.

## II. Comparison of QM and MM minimum energy structures

NOTE: This section walks through NAMD minimization before QM minimization.

If you want QM calcns on your input structure to CGenFF, the `init_psi4/opt_mmff.py` script may be helpful. 

It uses the Quanformer package: .

However, instead of installing the package, you can download the relevant modules from Github and call similar to [here](https://github.com/vtlim/off_psi4/blob/master/examples/frozen_atoms/example.py).

6. [`./init_namd/`] Minimize in NAMD. 

    * Do this prior to full scan bc starting Marvin coordinates are garbage.

7. Analyze minimized MM structure in VMD. This will be used as input for QM.

    * Load the `.psf` file and minimized `.coor` file.

    * If structure needs manual rearrangement (e.g., if not planar when you know it should be, or if you want to consider additional conformations)

        * VMD move atom: press `5`, click atom, move atom with mouse.

        * VMD move group of atoms: create new representation (`Graphics` > `Representations`) with selected atoms, press `9`, rotate/translate with mouse.

        * [VMD manual](https://www.ks.uiuc.edu/Research/vmd/current/ug/node33.html)

    * For each structure, `File` > `Save coordinates` > select `all` atoms. Save as `.pdb` or `.xyz` format.

8. [`./init_psi4/`] Geometry minimize with QM using Psi4.

    * Directly lifted coordinates from previous step for Psi4 input file. 

9. Compare minimized structures from steps 6 and 8 in VMD.

    * Based on agreement of minima structures, you may need to change atom types. In that case, remember to regenerate the psf file (step 4).

    * When I added improper terms in str file, it wasn't recognized by psfgen. So I modified the generated PSF directly.

        * In the `2 !NIMPHI: impropers` subheading, I added the atom numbers for new impropers (4 atoms/improper).

        * Also incremented subheader value next to NIMPHI by number of impropers added.

        * See example in `01_setup/psfgen/` comparing the PSF in `psfgen-02` and `psfgen-03` .

    * Also had to fix some of the atom name columns in the last column of generated PDB file bc some were missing.

## III. Comparison of QM and MM dihedral scan profiles

10. Analyze molecule to prepare for dihedral scan.

    * Identify atoms to be rotated.

        * Example: H9, N5, C8, N4, H8, H7, H6, not N3

    * Identify PDB numbers corresponding to above.

        * Example: 22 13 11 12 21 20 19

    * Determine which atoms will define dihedral angle.

        * Example: N2 C7 N3 C8 (8 9 10 11)

11. [`./01_setup/`] Generate structures for dihedral scan.

    * Subtract 1 from PDB numbers for use in Tcl script with VMD, and for NAMD

    * But use the PDB numbers as in when restraining in Psi4

    * Edit and run `01_setup-dihedrals.tcl`

        * Name of input PDB

        * Where output PDBs are written

        * Atom numbers of whole group to be rotated

        * Atom numbers of the four atoms to define dihedral. 

            * NOTE: Order matters. Atoms should be listed in order, with central atoms in middle. If [A B C D] does not work, try [D C B A].

    * Edit and run `02_pdbPsiInput.sh`

        * Main directory location

        * Name of theory subdirectory

        * Atom numbers to be frozen

        * Method and basis set used

        * Any other desired QM parameters

    * Edit and run `03_NAMDinput.sh`

        * Main directory location

        * Name of reference input file

        * Atom numbers of the dihedral for restraint

12. Run the QM and MM jobs.

13. [`./02_analysis/02_parse-diheds`] Analyze scans.

    * Get NAMD dihedral output angle from .coor files.

        * `vmdt -e ../12_analysis/get_namd_diheds.tcl -args /DFS-B/DATA/mobley/limvt/3_neutral/11_setup-namd/psfgen-03/gbin_psfgen.psf 7 8 9 10`

        * May want to sort resulting dat file (in vim: `:sort n`).

    * Compute/draw the profiles.

        * `python dihed_parser.py --qdir /path/to/qm_results/ --qfile output.dat --mdir /path/to/mm_results/ --mfile minimize.out --show --save`

14. [`./02_analysis/03_view`] View results.

    * TODO: add view scripts

## Notes to VTL

Sources of example materials:

 * PSF: `/DFS-B/DATA/mobley/limvt/3_neutral/11_setup-namd/psfgen-03/gbin_psfgen.psf`

 * PDB: `/DFS-B/DATA/mobley/limvt/3_neutral/init_namd2/03_point-out/final.pdb`

 * init NAMD input: `/DFS-B/DATA/mobley/limvt/3_neutral/init_namd2/minimize.inp`

 * init Psi4 input: `/DFS-B/DATA/mobley/limvt/3_neutral/init_psi4/01_mp2-631Gd/input.dat`

 * dihed NAMD input: `/DFS-B/DATA/mobley/limvt/3_neutral/dihed_namd`

 * dihed Psi4 input: `/DFS-B/DATA/mobley/limvt/3_neutral/dihed_psi4`