residues that form water-mediated hydrogen bonds to the drug
molecule (“resid 136 330”).- For more information on using VMD, including documentation
and tutorials, visit the VMD software webpage (http://www.ks.
uiuc.edu/Research/vmd).
Step 3. Obtain force field files.- Download CHARMM36 by visiting the CHARMM force field
webpage (http://mackerell.umaryland.edu/charmm_ff.shtml). - Unarchive the file contents (toppar) into your working
directory.
Step 4. Obtain drug parameters.- Open VMD’s command line tool by clickingExtensions!Tk
Console in theVMD Mainwindow. - Ensure that you are operating within your working directory by
entering the following command:
cd - Save a PDB file of the drug molecule by entering the following
commands:
set drug [atomselect top "resname TYL"] ; # Select drug molecule
$drug set segname TYL ; # Assign segname for psfgen
$drug writepdb TYL.pdb ; # Write segment PDB - Launch Maestro and load the drug PDB file generated with
VMD by clickingFile!Import Structures...and selecting TYL.
pdb (Fig.6). - Flag double bonds in the drug structure by right clicking them
and selectingIncrease Bond Order. For reference,seeFig. 2, left. - Fill remaining open valencies in the drug structure by left click-
ing and dragging a box around the molecule and clicking
Edit!Add Hydrogens. - Save a MOL2 file of the drug molecule by clickingFile!Export
Structures.... Enter theFile nameas “TYL” selectFiles of typeas
MOL2 (*.mol2). - Visit the ParamChem server (https://cgenff.paramchem.org)
and click onMy Account!Registerto create an account. After
activating your ParamChem account, click on My
Account!Loginto log in. - Submit the drug structure to the ParamChem server by clicking
on theUpload Moleculetab, selectingFilenameTYL.mol2, then
clicking theUpload Filebutton. - Save the TYL.str file provided underOutputto your working
directory.
254 Jodi A. Hadden and Juan R. Perilla