molUP

molUP is a free VMD extension that allows you to open and save Gaussian files. This tool can be used to analyze results from Gaussian output files and prepare Gaussian input files.

molUP provides also a set of tools to adjust bond lengths, rotate angles and dihedral angles directly on VMD. With molUP, it is possible to add and remove atoms or molecules using VMD. 

H. S. Fernandes, M. J. Ramos, N. M. F. S. A. Cerqueira J. Comput. Chem. 2018, 39, 1344–1353. DOI: 10.1002/jcc.25189

Installation

molUP can be easily installed through the VMD Store.
Please, install the VMD Store and then this extension.
Available for macOS, Linux, and Windows

Download vmdStore

For manual installation check the instructions below. 

 

Introduction

molUP is a VMD extension that provides a simple manner for loading and saving Gaussian files, and analyze related results. molUP provides a graphical interface for VMD where the users can load and save chemical structures in the Gaussian file formats. This extension includes a set of tools to set up any calculation supported by Gaussian, including ONIOM; analyze energies through interactive plots; animate vibrational frequencies; draw the vectors associated with those frequencies; modify bonds, angles, and dihedrals; and collect bibliographic information on the employed methods.

Features

Open Files

molUP open Gaussian input and output files on VMD. In the case of calculations of structure optimizations, molUP allows the user to choose which structure or structures must be loaded.

Moreover, molUP can handle structures from any type of file supported by VMD such as PDB, XYZ, AMBER…

Save Files

The structures can be saved as a new Gaussian input file, PDB, XYZ or an ORCA input  NEW  file. 

ONIOM Layers

molUP is prepared to handle with ONIOM calculation with 2 or 3 layers (High, Medium, and Low Layers).

This is an interactive interface to choose which atoms must be assigned to each layer.

molUP will automatically fill the valence across the boundary of adjacent layers with hydrogens as link atoms.

Fix the position of some atoms

A similar interface is used to select atoms that must be fixed during the structure optimization calculations.

The atoms can be selected using the table interface or through the atom selection style of VMD. 

Charges

molUP provides a table containing information about the Molecular Mechanics charge of all atoms in the system. 

The charges can be manually edited in this interface.

Update charges from a Gaussian output file. NEW 

Prepare a Gaussian input file

This tab on molUP’s interface allows the preparation of every section of a Gaussian Input file:

  • Job Title
  • Calculations keywords (Using default or custom inputs)
  • Charge and Spin Multiplicity of the System
  • Connectivity (can be imported from VMD, Gaussian input files or assigned manually)
  • Parameters and Other Information (Useful to provide MM parameters, which can be imported from PRMTOP files, use pseudo-potentials or set up a scan using the embedded modredundant assistant)
Show charged molecules

molUP quickly identifies the positive and negatively charged molecules in the system (blue and red surfaces)

After the assigning of ONIOM layers, this interface can also be used to estimate the charge of each layer (required for any QM/MM calculation).

Modify bonds, angles, and dihedral angles

molUP provides a set of three tools to modify bond lengths, angle amplitudes, and dihedral angle torsions

Use the mouse to pick the atoms and the pop-up window to move the atoms that can be custom selected

Add and Remove Atoms/Molecules  NEW 

molUP introduces a new tool to add atoms and molecules to your system. You can add molecules from the fault molecule or picking each atom from the periodic table.

Simply choose the atom/molecule and pick an atom of your initial system. The new atom/molecule will be placed in relation to that picked atom. You can adjust the position and orientation of the new atom/molecule. 

Moreover, you can now delete atoms on VMD simply picking them. 

Scans of reaction coordinates

When a reaction coordinate scan is performed, we are interested in the energy profile of a certain reaction or conformational rearrangement. Therefore, molUP plots the energy of each optimized structure to easily study the energy profile and analyze the structures of each step. 

The energy plot is interactive so each point can be selected to see the related structure. 

Several options are available to zoom, change the energy units, and split the ONIOM energy.

Frequency calculations

Every transition state (TS) must be validated through a frequency calculation that must result in a single imaginary frequency (negative value) assigned to the atoms involved in the reaction. 

This task becomes easier with molUP that collects all the frequencies and shows the vectors associated with that vibrational profile.

molUP also provides an animation of the vibration of the atom involved in each frequency.

This frequency calculation is also important to provide Thermal Corrections that are needed to estimate the Gibbs free energy. 

What publications should I cite?

molUP evaluated the type of calculations that were performed to collect a list of publications that must be cited according to the methods and software used.

If you notice that a particular citation is missing, please contact us: hfernandes@med.up.pt

 

Tutorials

How to start a QM/MM study from a Molecular Dynamics (MD) simulation? [See Tutorial]


Minimum Requirments

Operating System: macOS, Linux, or Windows.

Visual Molecular Dynamics (VMD) 1.9.3 (Free Download) or later.


Installation

Automatic Installation

You could easily install molUP through the VMD Store.   Download vmdStore

Manual Installation

Alternatively, you could install molUP manually:

  1. Download or Clone the repository.
  2. Copy the molUP directory to a location on your computer. (Get that location!)
  3. Copy the text inside “install.txt” file and paste on your .vmdrc file (macOS and Linux ) or vmd.rc file (Windows).
  4. Replace the string “$::vmdStorePath/plugins/molUP” by your installation location (Step 2).
  5. Save the .vmdrc or vmd.rc file.
  6. Restart VMD.

(Optional) Run molUP from bash

molUP supports now the loading of Gaussian files directly from your command line (available for macOS and Linux).

Tutorial:

  1. Add the following line to your .bashrc (Linux) or .bash_profile (macOS) file. (This file is located in the HOME directory) You have to edit the “path of the bashScript.tcl file” field by the complete path of this file that is located in the molUP installation directory: “molUP/lib/bashScript.tcl”
alias molUP='vmd -e "path of the bashScript.tcl file" -args'
  1. Call molUP from the command line:

Open a Gaussian file using the standard procedure:

molUP "Gaussian file"

Open a Gaussian output file reading all available structures:

molUP "Gaussian file" -all

Report Bugs/Suggestions

If you experienced any type of issue, please contact us to fix it as soon as possible. (Provide the error message and the file that causes it.)

If you have any idea of new features, please let us know to try the implementation in a future version.

E-Mail: hfernandes@med.up.pt


If you used molUP, please cite

H. S. Fernandes, M. J. Ramos, N. M. F. S. A. Cerqueira J. Comput. Chem. 2018, 39, 1344–1353. DOI: 10.1002/jcc.25189

Download citation


Changelog

Version 1.5.3 (30 OUT 2018)
– [Bug fixed] An issue that hides the button “Add” on the “Add Molecule/Fragment” window of the “Add Atoms” tool.

Version 1.5.2 (18 OUT 2018)
– [New feature] A button was added to allow the import of new calculated charges from Gaussian output files.
– [New feature] Atoms can now be picked to assign them to an ONIOM layer or to change its freezing state during optimization calculations.
– [Minor Change] The charge and multiplicity are now loaded from the Gaussian file instead of being calculated ad the beginning.
– [Bug fixed] Fixed the issue that prevented the VMD citation appears in the references list.

Version 1.5.1 (6 SEP 2018)
– [Minor Changes] Now all the internal packages have their own versions.

Version 1.5.0 (1 AUG 2018)
– [New feature] molUP now supports saving ORCA Input files.

Version 1.4.12 (31 JUL 2018)
– [Bug fixed] Now, the link atoms are placed at the correct distance when custom selections are used to save new Gaussian Input Files.

Version 1.4.11 (19 JUN 2018)
– [Bug fixed] Elements with two characters were incorrectly saved when new Gaussian input files were generated.

Version 1.4.10 (18 JUN 2018)
– [Bug fixed] Fixed an issue that misunderstanding the elements when new Gaussian input files are saved.

Version 1.4.9 (21 MAY 2018)
– [Bug fixed] Fixed an issue that prevents the loading of multiple files using molUP.

Version 1.4.8 (17 MAY 2018)
– [Bug fixed] Fixed an issue that prevents the loading of PRMTOP files that could present an unusual format.

Version 1.4.7 (16 MAY 2018)
– [Improvement] Significant improvement of the procedure that imports the PRMTOP file.

Version 1.4.6 (15 MAY 2018)
– [New feature] A “-all” flag was added to the molUP bash command. This new feature is allow the loading of all structures of a any Gaussian Output file.
– [Bug fixed] Fixed an issue that precluded the conversion of certain AMBER parameters from PRMTOP files.

Version 1.4.5 (10 MAY 2018)
– [Bug fixed] Fixed an issue that does not allow the correct export of the energy data from energy profiles.

Version 1.4.4 (9 ABR 2018)
– [Bug fixed] Fixed an issue that originated an error when modification tools were used after the addition or deletion of atoms.
– [Bug fixed] Fixed an issue that generated random behavior when modification tools were used.

Version 1.4.3 (9 ABR 2018)
– [Bug fixed] Fixed an issue that changes the connectivity when a new molecule is loaded.

Version 1.4.2 (5 ABR 2018)
– [Bug fixed] Fixed an issue that prevents the visualization of frequencies.

Version 1.4.1 (3 ABR 2018)
– [Bug fixed] Fixed an issue that changed the view during the process to add and/or remove atoms.
– [Bug fixed] Fixed an issue that displayed an error message when the user clicked on “Delete” and no atom had been selected.

Version 1.4.0 (3 ABR 2018)
– [New feature] Now you can delete and add atoms using molUP.
– [Improvement] The footer toolbar includes a shortcut button to enable the Add/Remove Bonds mouse mode, and two icons to use the new tools that enable the addition and deletion of atoms.

Version 1.3.10 (9 MAR 2018)
– [Bug fixed] Fixed a bug that prevented the selection of the last three frequencies.

Version 1.3.9 (7 MAR 2018)
– [Bugs fixed] Minor bugs fixed
– [New feature] Add custom selections in the modification (bonds, angles, and dihedral angles) tools

Version 1.3.8 (5 MAR 2018)
– [Bug fixed] Fixed an issue that gave an error collection energies from the last structure of certain Gaussian output files.

Version 1.3.7 (2 MAR 2018)
– [New feature] Load multiple structures at once.

Version 1.3.6 (23 FEV 2018)
– [New feature] New procedure to initiate molUP and load a Gaussian file from the command line in macOS and Linux. See documentation to know how to implement this new feature.

Version 1.3.5
– [Bug fixed] Fixed an issue that prevented the loading of connectivity from a Gaussian Input File.
– [Bug fixed] Fixed an issue that prevented the loading of scan that finished with “Normal Termination”.

Version 1.3.4 (9 FEV 2018)
– [Bug fixed] Fixed the issue that prevented the file saving.
– [Bug fixed] Files are no correctly formatted to Gaussian software when they are saved on Windows.

Version 1.3.3 (8 FEV 2018)
– [Improvement] Huge files are now quickly loaded on molUP through a rationalization of the loading process.

Version 1.3.2 (6 FEV 2018)
– [Bug fixed] Atoms are now colored by element instead of Name to fix the issue that miscolored the atoms after a molecule deletion.
– [Bug fixed] Error message windows were not loading correctly.
– [Bug fixed] The user gets the control over the blank lines between the connectivity and parameters sections.

Version 1.3.1 (2 FEV 2018)
– [New feature] Now, molUP will only load the first 15 frequencies (up to 5x faster). The user can load all the structures clicking on the “Load All Freqs” button.

Version 1.3.0 (2 FEV 2018)
– [Improvement] The way the files are loaded on molUP was improved (up to 2x faster).

Version 1.2.2 (1 FEV 2018)
– [Bug fixed] This update fixes an issue that prevented a correct load of Gaussian Input files.

Version 1.2.1 (31 JAN 2018)
– [Bug fixed] The user gets the control over the blank lines between the connectivity and parameters sections.

Version 1.2.0 (31 JAN 2018)
– [New feature] molUP is now compatible with Windows OS. The compatibility was possible thanks to the open source tool Cygwin (http://www.cygwin.com).

Version 1.1.2 (29 JAN 2018)
– [Bug fixed] The scrollbar of the parameters sections was scrolling on connectivity section.
– [Bug fixed] Link atoms were not written in the input file when the adjacent atoms had no hydrogen atom bonded.

Version 1.1.1 (27 OUT 2017)
– [Bug fixed] Fixed an issue that prevents bonds, angles, and dihedral angles modification of single atoms.

Version 1.1.0 (20 JUL 2017)
– [New feature] molUP provides a new tool to easily setup scans (ModRedundant) of bonds, angles, and dihedrals. This new tool is available in the “Other Informations” menu within the “Input” tab.

Version 1.0.11 (20 JUL 2017)
– [Bug fixed] Fixed a issue that returns an error when a scan has onyl one structure to load.

Version 1.0.10 (19 JUL 2017)
– [New feature] New tool to help users to measure bond, angles, and dihedral angles. Available in the “Tools” menu.
– [New feature] New dialog alert when the loaded output file does not finish with the Normal termination message.
– [Bug fixed] Fixed error that occurs when no optimized structure is founded during the load of an output file using the “All optimized structures” option.

Version 1.0.9 (18 JUL 2017)
– [New feature] Several features were added to the energy section namely energy units adjustment, set zero for the energy of the first structure, and choose which layer must be plotted.
– [New feature] Files missing information about layer and/or freeze status will be automatically set “H” and/or “0”, respectively.
– [Bug fixed] Fixed a bug that prevents the correct work of the Methodology GUI.

Version 1.0.8 (17 JUL 2017)
– [New feature] The list of basis set was updated to include all the basis sets available in Gaussian software (http://gaussian.com/basissets/). Users can also add more basis set or keywords by their own.

Version 1.0.7 (14 JUL 2017)
– [Big fixed] The section for setting up charges and spin multiplicity updates every time you change the layer system.
– [New feature] The list of bibliographic references, methodology texts, and calculations setup are now available on a folder (/user/) that can be modified by users to fit their needs.
– [New feature] The Layer, Freeze and Charges sections were placed on an individual category called “Structure”.

Version 1.0.6 (16 JUN 2017)
– [New feature] The selected point on the energy graph is now more visible.

Version 1.0.5 (8 JUN 2017)
– [Bug fixed] Fix an error that prevents loading files missing the AtomType Information.
– [Bug fixed] Recalculate connectivity when no information is provided on the input file.

Version 1.0.4 (14 APR 2017)
– [Bug fixed] Fix an error when MM calculations were loaded on molUP

Version 1.0.3 (6 APR 2017)
– [New feature] New option that allows to rewrite the connectivity section based on current VMD connectivity.

Version 1.0.2 (3 APR 2017)
– [New feature] Redesign of the interface of charge and spin multiplicity setup section.
– [Bug fixed] Fix a bug that prevents the correct show up of references that must be cited according to the type of calculations.

Version 1.0.1 (31 MAR 2017)
– [New feature] Set of default calculation types were release. The user can also create their own keywords sections.
– [Minor fix] Redesign of the input section.
– [New feature] Info icons were added to some molUP’s sections.

Version 1.0 (30 MAR 2017)
– [New feature] Load energies for all structures
– [New feature] The energy value is presented every time the user clicks on the graph
– [New feature] Selected point of the energies graph is green outlined
– [New feature] Info icons were added to provide additional explanation about relevant concepts
– [new feature] Thermal Corrections are collected from frequency calculations, and the zero-point energy, enthalpy, and Gibbs free energy are calculated
– [New feature] Copy button nearby the fields with relevant information, i.e. energies
– [New feature] List of references that must be cited according to the type of calculations performed by the user
– [New feature] List of standard methodology texts to help user during the article writing process
– [Bug fixed] Residues are correctly assigned now

Version 0.2.5 (27 MAR 2017)
– [New feature] Load AMBER parameters from PRMTOP file
– [Bug fixed] Update the icon of the bond modification tool

Version 0.2.4 (17 MAR 2017)
– [Bug fixed] Floating numbers on freeze status were converted to integers when saved

Version 0.2.3
– [Bug fixed] Fix an error that causes a GUI problem when a molecule is deleted.
– [Bug fixed] Fix an error that prevents negative and positively charged residues to show

Version 0.2.2
– [Bug fixed] Fix a bug that prevents the load of some multistructures files.
– [New feature] “Drag and Drop” to zoom in and right-click to zoom out on the energetic profile.

Version 0.2.1
– [Bug fixed] Remove trace variables when the molUP window is closed.

Version 0.2.0
– [New feature] Advanced options were added to the save window. Now you can save some parts of the system.

Version 0.1.9
– [New feature] molUP will apply automatically connectivity or .log files based on the available .com file (should be located at the same folder) The options to load from another file or rebond are still available.

Version 0.1.8
– [Bug fixed] Molecules containing less than 250 atoms will be presented by Licorice instead of lines in the “All” representation.
– [New feature] Play and Pause buttons were added to the frequency animation interface
– [New feature] A slider was included to choose the vector’s size threshold for representation
– [New feature] Non-optimized structures will be colored by red on the energetic profile graph

Version 0.1.7
– [Bug fixed] Automatic zoom for a huge number of structures (load all optimized structures)

Version 0.1.6
– [New feature] Help balloons will appear when the mouse hovers the buttons

Version 0.1.5
– [Bug fixed] Link atom assignment was fixed
– Remove the Close icon on File Menu (Redundant button)
– [New feature] Changelog information was added to About Menu

Version 0.1.4
– [Bug fixed] Transient windows (bond modify, angle, …) were programmed to keep on top every time
– [Bug fixed] Fixed an error that prevents the load of files in a certain stage of the calculation
– [Bug fixed] Fix an error that prevents the load of structures with an energy value of *****************
– [Bug fixed] Freq animation error when more than one structure is loaded.

Version 0.1.3
– [Bug fixed] Atoms without charges are correctly loaded
– [Bug fixed] Keywords tagged by yellow cannot be read. They were changed to grey
– [New feature] A color chooser for frequency vectors

Version 0.1.2
– [Bug fixed] All atoms are considered during frequency animations
– [Bug fixed] List of frequencies is cleared before a new molecule is loaded
– [Bug fixed] “_” and other non-numeric characters are ignored when RESID is read

Version 0.1.0
– Release (alpha testers)

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