@@ -144,7 +144,7 @@ @Article{Ester96
 }
 
 @Article{Roe13,
-  author = {Roe, Daniel R. and Cheatham, III, T.E.},
+  author = {Roe, Daniel R. and Cheatham, III, Thomas E.},
   title = {{PTRAJ and CPPTRAJ: Software for Processing and Analysis of 
             Molecular Dynamics Trajectory Data}},
   journal = {J. Chem. Theory Comput.},
@@ -241,7 +241,7 @@ @Article{Hunenberger1995
 }
 
 @Article{Galindo2015,
-  author = {Galindo-Murillo, Rodrigo and Roe, Daniel R. and Cheatham, III, T.E.},
+  author = {Galindo-Murillo, Rodrigo and Roe, Daniel R. and Cheatham, III, Thomas E.},
   title = {{Convergence and reproducibility in molecular dynamics simulations
             of the DNA duplex d(GCACGAACGAACGAACGC)}},
   journal = {Biochim. Biophys. Acta},
@@ -426,3 +426,9 @@ @article{Chen2021
 year = {2021}
 }
 
+@article{Roe2022,
+author = {Roe, Daniel R. and Bergonzo, Christina},
+journal = {Journal of Computational Chemistry},
+title = {{PrepareForLeap: An Automated Tool for Fast PDB-to-Parameter Generation}},
+year = {2022}
+}
@@ -7149,8 +7149,11 @@ prepareforleap crdset <coords set> [frame <#>] name <out coords set>
 \end_layout
 
 \begin_layout LyX-Code
-                  	[nowat [watermask <watermask>] [noh] [keepaltloc {<alt
- loc ID>|highestocc}]
+                  	[nowat [watermask <watermask>] [noh]
+\end_layout
+
+\begin_layout LyX-Code
+                      [keepaltloc {<alt loc ID>|highestocc}]
 \end_layout
 
 \begin_layout LyX-Code
@@ -7191,8 +7194,11 @@ prepareforleap crdset <coords set> [frame <#>] name <out coords set>
 \end_layout
 
 \begin_layout LyX-Code
-                  	  sugarmask <sugarmask> [noc1search] [nosplitres] [resmapfile
- <file>]
+                  	  sugarmask <sugarmask> [noc1search] [nosplitres]
+\end_layout
+
+\begin_layout LyX-Code
+                        [resmapfile <file>]
 \end_layout
 
 \begin_layout LyX-Code
@@ -7391,7 +7397,7 @@ id> or the location with the highest occupancy if
 \end_layout
 
 \begin_layout Description
-[dterminemolmask
+[determinemolmask
 \begin_inset space ~
 \end_inset
 
@@ -7555,6 +7561,13 @@ resmapfile
 This command will prepare a structure (usually from a PDB) for processing
  with the Amber program LEaP to generate topology and coordinates files
  for MD simulations.
+\begin_inset CommandInset citation
+LatexCommand citep
+key "Roe2022"
+literal "true"
+
+\end_inset
+
  It will handle things like choosing alternate atom locations, removing
  waters/hydrogen atoms from the structure, renaming residues and generating
  'bond' commands for disulfide bonds, change histidine names based on any
 
@@ -3121,7 +3121,8 @@ void Exec_PrepareForLeap::Help() const
           "\t[pdbout <pdbfile> [terbymol]]\n"
           "\t[leapunitname <unit>] [out <leap input file> [runleap <ff file>]]\n"
           "\t[skiperrors]\n"
-          "\t[nowat [watermask <watermask>] [noh] [keepaltloc {<alt loc ID>|highestocc}]\n"
+          "\t[nowat [watermask <watermask>] [noh]\n"
+          "\t[keepaltloc {<alt loc ID>|highestocc}]\n"
           "\t[stripmask <stripmask>] [solventresname <solventresname>]\n"
           "\t[molmask <molmask> ...] [determinemolmask <mask>]\n"
           "\t[{nohisdetect |\n"
@@ -3131,7 +3132,8 @@ void Exec_PrepareForLeap::Help() const
           "\t  existingdisulfides |\n"
           "\t  [cysmask <cysmask>] [disulfidecut <cut>] [newcysname <name>]}]\n"
           "\t[{nosugars |\n"
-          "\t  sugarmask <sugarmask> [noc1search] [nosplitres] [resmapfile <file>]\n"
+          "\t  sugarmask <sugarmask> [noc1search] [nosplitres]\n"
+          "\t  [resmapfile <file>]\n"
           "\t  [hasglycam] [determinesugarsby {geom|name}]\n"
           "\t }]\n"
           "  Prepare the structure in the given coords set for easier processing\n"