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  • DelEnsembleElec Tutorial: Installation
    loaded files for instance prmtop and psf files This plugin requires DelPhi to run You will need to download Delphi directly from the developers at the following link Download Delphi here UNIX INSTALLATION Instructions unzip the tarball to a directory of your choice by using this command tar xzf delenselec tgz your directory here add these two lines of code to your vmdrc file usually located in your directory If you do not have one download a sample vmdrc file set auto path auto path your directory here delenselec1 0 NOTE this may require the full pathname vmd install extension delphielec delphielec tk cb Analysis DelEnsembleElec Note if you have write permissions to the VMD plugin folder you can simply add the delenselec1 0 folder to the directory plugins noarch tcl and you only need the second of the above two lines placed into your vmdrc file Another Note You must have the line menu main on in your vmdrc file or else VMD will not work properly Now open VMD to see if it works Click Extensions Analysis DelEnsembleElec WINDOWS INSTALLATION Instructions unzip the tarball to the plugin directory probably located somewhere like C Program Files University of Illinois

    Original URL path: https://amarolab.ucsd.edu/delphielectut/de_installation.html (2015-07-15)
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  • DelEnsembleElec Tutorial: Single Frame
    finished option is selected Go to the menubar Edit Input File The Edit Delphi Input File window will appear Click the button Load Template Param File Navigate to the file param in Click Open The Size File and Charge File fields must point to the proper siz and crg parameter files that is included in this tutorial or may be downloaded at Clemson s Website http www ces clemson edu

    Original URL path: https://amarolab.ucsd.edu/delphielectut/de_singleframe.html (2015-07-15)
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  • DelEnsembleElec Tutorial: Ensemble-Averaged
    top left corner says protein Below that select the Backbone checkbox Make sure the checkbox labelled Trajectory is selected with Frame ref set to 0 Click the Align button to align every frame of the protein to the first frame Close the RMSD Trajectory Tool Window Start the Delphi run In the VMD Main window select Extensions Analysis DelEnsembleElec The DelEnsembleElec plugin window will appear Under the option box Select molecule for Delphi run select 1 cpaf prmtop In the Selection textbox leave the value at protein In the Write to Output textbox change the value to traj cpaf cube Deselect the Load into VMD when finished option and instead select Load first frame colored by charge Go to the menubar Edit Input File The Edit Delphi Input File window will appear Click the button Load Template Param File Navigate to the file param in Click Open As before the Size File and Charge File fields must point to the proper siz and crg parameter files that came with your Delphi package or may be downloaded at Clemson s Website http www ces clemson edu compbio delphi html Click OK to close the Edit Delphi Input File window Note The trajectory provided in this tutorial has 100 frames so the entire run will probably take 100 times longer than the single frame calculation done in the previous section potentially amounting to hours or days The results of a completed run of this tutorial s trajectory has been provided in the tutorial files If you would like to perform the calculation yourself click the Run Delphi button Otherwise 11 In the VMD main window go to File New Molecule 12 The Molecule File Browser window will appear Under the Load Files for list box select 0 cpaf prmtop 13 Click Browse

    Original URL path: https://amarolab.ucsd.edu/delphielectut/de_ensembleavg.html (2015-07-15)
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  • DelEnsembleElec Tutorial: Troubleshooting
    must manually enter the location of Delphi by going to Edit Settings Then specify the proper path name in the Delphi Directory text box If you get errors to the effect of Missing charge parameter file or Missing size parameter file keep in mind that both of these must be specified or else neither And in cases where VMD cannot read charge or radius information directly from the loaded molecule

    Original URL path: https://amarolab.ucsd.edu/delphielectut/de_troubleshooting.html (2015-07-15)
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  • and axes axes location off stage location off position and turn on menus menu main on menu graphics on menu files on menu main move 5 196 menu graphics move 5 455 menu files move 1300 750 display projection orthographic

    Original URL path: https://amarolab.ucsd.edu/delphielectut/.vmdrc (2015-07-15)
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