diff --git a/doc/htmlize b/doc/htmlize
index 4f06516936..6916227bce 100755
--- a/doc/htmlize
+++ b/doc/htmlize
@@ -161,7 +161,7 @@ foreach document ($1)
echo "htmlize: Compressing copies of postscript source"
foreach file (${document}*.ps)
if (-e $file) then
- compress < $file > ${document}/${file}.Z
+ gzip < $file > ${document}/${file}.gz
@ compress_stat += $status
endif
end
diff --git a/doc/user/fileformats.tex b/doc/user/fileformats.tex
index 7bed7c8d35..c739f46599 100644
--- a/doc/user/fileformats.tex
+++ b/doc/user/fileformats.tex
@@ -1,12 +1,12 @@
%
-% $Id: fileformats.tex,v 1.6 2006-09-28 14:36:53 d3j191 Exp $
+% $Id: fileformats.tex,v 1.7 2007-04-10 23:43:18 bylaska Exp $
%
\label{sec:formats}
-%\section {Format fragment file}
+\section {Format fragment file}
\begin{table}[h]
\begin{center}
-\begin{tabular}{p{15mm}p{12mm}l}
+\begin{tabular*}{150mm}{p{15mm}p{12mm}l}
\hline\hline
Card & Format & Description \\ \hline
I-1-1 & a1 & \$ to identify the start of a fragment \\ % $ for emacs
@@ -53,7 +53,7 @@ II-1-9 & i5 & polarization group\\
II-1-10 & f12.6 & atomic partial charge\\
II-1-11 & f12.6 & atomic polarizability\\
\hline
-\mc{3}{l}{For each additional parameter set on card II-2}\\
+For each additional parameter set on card II-2\\
\hline
II-2-1 & 11x,a6 & atom type\\
II-2-2 & a1 & dynamics type\\
@@ -70,9 +70,9 @@ connectivity} \\
\hline
III-1-1 & 16i5 & connectivity, duplication allowed\\
\hline
-\mc{3}{l}{One blanc card to signal the end of the connectivity list}\\
+One blanc card to signal the end of the connectivity list\\
\hline
-\mc{3}{l}{For each z-matrix definition one card IV}\\
+For each z-matrix definition one card IV\\
\hline
IV-1-1 & i5 & atom i \\
IV-1-2 & i5 & atom j \\
@@ -82,12 +82,12 @@ IV-1-5 & f12.6 & bond length i-j\\
IV-1-6 & f12.6 & angle i-j-k\\
IV-1-7 & f12.6 & torson i-j-k-l\\
\hline\hline
-\end{tabular}
+\end{tabular*}
\caption{The format of fragment files.\label{tbl:nwmdfrg}}
\end{center}
\end{table}
-%\section {Format segment file}
+\section {Format segment file}
\begin{table}[h]
\begin{center}
@@ -112,7 +112,7 @@ I-3-6 & i5 & number of z-matrix definitions\\
I-3-7 & i5 & number of parameter sets \\
1-3-8 & i5 & default parameter set\\
\hline
-\mc{3}{l}{For each prarmeter set one card I-4}\\
+For each prarmeter set one card I-4\\
\hline
I-4-1 & f12.6 & dipole correction energy \\
\hline
@@ -141,7 +141,7 @@ II-1-5 & i5 & \\
II-1-6 & i5 & charge group\\
II-1-7 & i5 & polarization group\\
\hline
-\mc{3}{l}{For each parameter set one card II-2}\\
+For each parameter set one card II-2\\
\hline
II-2-1 & 5x,a5 & atom type \\
II-2-2 & a1 & dynamics type\\
@@ -174,7 +174,7 @@ III-1-5 & i5 & bond parameter origin\\
& & 0: from database, next card ignored \\
& & 1: from next card\\
\hline
-\mc{3}{l}{For each parameter set one card III-2}\\
+For each parameter set one card III-2\\
\hline
III-2-1 & f12.6 & bond length in nm\\
III-2-2 & e12.5 & bond force constant in kJ nm$^2$ mol$^{-1}$\\
@@ -200,7 +200,7 @@ IV-1-6 & i5 & angle parameter origin\\
& & 0: from database, next card ignored \\
& & 1: from next card\\
\hline
-\mc{3}{l}{For each parameter set one card IV-2}\\
+For each parameter set one card IV-2\\
\hline
IV-2-1 & f10.6 & angle in radians\\
IV-2-2 & e12.5 & angle force constant in kJ mol$^{-1}$\\
@@ -227,7 +227,7 @@ V-1-7 & i5 & proper dihedral parameter origin\\
& & 0: from database, next card ignored \\
& & 1: from next card\\
\hline
-\mc{3}{l}{For each parameter set one card V-2}\\
+For each parameter set one card V-2\\
\hline
V-2-1 & i3 & multiplicity\\
V-2-2 & f10.6 & proper dihedral in radians\\
@@ -255,7 +255,7 @@ VI-1-7 & i5 & improper dihedral parameter origin\\
& & 0: from database, next card ignored \\
& & 1: from next card\\
\hline
-\mc{3}{l}{For each parameter set one card VI-2}\\
+For each parameter set one card VI-2\\
\hline
VI-2-1 & 3x,f10.6 & improper dihedral in radians\\
VI-2-2 & e12.5 & improper dihedral force constant in kJ mol$^{-1}$\\
@@ -269,7 +269,7 @@ VI-2-2 & e12.5 & improper dihedral force constant in kJ mol$^{-1}$\\
\begin{center}
\begin{tabular*}{150mm}{p{15mm}p{12mm}l}
\hline\hline
-\mc{3}{l}{For each z-matrix definition one card VII}\\
+For each z-matrix definition one card VII\\
\hline
VII-1-1 & i5 & atom i \\
VII-1-2 & i5 & atom j \\
@@ -284,7 +284,7 @@ VII-1-7 & f12.6 & torson i-j-k-l\\
\end{center}
\end{table}
-%\section {Format sequence file}
+\section {Format sequence file}
\begin{table}[h]
\begin{center}
@@ -326,7 +326,7 @@ II-2-3 & i5 & number of times to repeat cards ($ncount$)\\
\end{center}
\end{table}
-%\section {Format trajectory file}
+\section {Format trajectory file}
\begin{table}[h]
\begin{center}
@@ -392,8 +392,18 @@ II-4-8 & l1 & logical lps for solute induced dipoles \\
II-4-5 & i10 & number of solvent molecules \\
II-4-6 & i10 & number of solvent atoms \\
II-4-7 & i10 & number of solute atoms \\
-\hline
-\hline
+\hline\hline
+\end{tabular*}
+\caption{Trajectory file format.\label{tbl:nwmdtrj}}
+\end{center}
+\end{table}
+
+
+\begin{table}[h]
+\begin{center}
+\begin{tabular*}{150mm}{p{15mm}p{12mm}l}
+\hline\hline
+Card & Format & Description \\ \hline
\mc{3}{l}{For each solvent molecule one card II-5 for each atom, if stardard precision} \\
\hline
II-5-1 & 3f8.3 & solvent atom coordinates, if lxw or lvw \\
@@ -420,11 +430,11 @@ II-6-4 & 3e12.6 & solute atom velocities, if lvs \\
II-6-7 & 3e12.6 & solute atom forces, if lfs (on new card if both lxs and lvs)\\
\hline\hline
\end{tabular*}
-\caption{Trajectory file format.\label{tbl:nwmdtrj}}
+\caption{continued trajectory file format.\label{tbl:nwmdtrj2}}
\end{center}
\end{table}
-%\section {Format free energy file}
+\section {Format free energy file}
\begin{table}[h]
\begin{center}
@@ -451,7 +461,7 @@ I-4-4 & e20.12 & average exponent forward perturbation energy at current $\lamb
\end{center}
\end{table}
-%\section {Format root mean square deviation file}
+\section {Format root mean square deviation file}
\begin{table}[h]
\begin{center}
@@ -486,7 +496,7 @@ III-2-3 & f12.6 & average segment rms deviation after superimposition \\
\end{center}
\end{table}
-%\section {Format property file}
+\section {Format property file}
\begin{table}[h]
\begin{center}
diff --git a/doc/user/user.search b/doc/user/user.search
index 356f7b38c6..c127c10ba9 100644
--- a/doc/user/user.search
+++ b/doc/user/user.search
@@ -19,8 +19,8 @@ Search:
PDF
-
Compressed postscript Part 1
-
Compressed postscript Part 2
+
Compressed postscript Part 1
+
Compressed postscript Part 2
Postscript Part 1
Postscript Part 2