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Update CHARMm and Amber documentation

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This commit is contained in:
Kurt Glaesmann 2009-07-06 18:25:58 +00:00
parent 0f3582955a
commit f3fe107366
4 changed files with 22 additions and 21 deletions
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10
doc/user/fileformats.tex
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@ -9,12 +9,7 @@
\begin{tabular}{p{15mm}p{12mm}l}
\hline\hline
Card & Format & Description \\ \hline
I-1-1 & a1 & \$ to identify the start of a fragment \\ % $ for emacs
I-1-2 & a10 & name of the fragment, the tenth character\\
& & N: identifies beginning of a chain\\
& & C: identifies end of a chain\\
& & blank: identifies chain fragment\\
& & M: identifies an integral molecule\\
I-1-1 & a1 & \$ or \# comments to describe fragment \\ % $ for emacs
\hline
I-2-1 & i5 & number of atoms in the fragment\\
I-2-2 & i5 & number of parameter sets\\
@ -70,7 +65,7 @@ connectivity} \\
\hline
III-1-1 & 16i5 & connectivity, duplication allowed\\
\hline
One blanc card to signal the end of the connectivity list\\
One blank card to signal the end of the connectivity list\\
\hline
For each z-matrix definition one card IV\\
\hline
@ -94,6 +89,7 @@ IV-1-7 & f12.6 & torson i-j-k-l\\
\begin{tabular*}{150mm}{p{15mm}p{12mm}l}
\hline\hline
Deck & Format & Description \\ \hline
I-0-1 & & \# lines at top are comments \\
I-1-1 & a1 & \$ to identify the start of a segment \\ %$ for emacs
I-1-2 & a10 & name of the segment, the tenth character\\
& & N: identifies beginning of a chain\\

14
doc/user/nwargos.tex
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@ -213,8 +213,9 @@ The source of the data is identified by \verb+$level$+, and can be
level & Description & Availability \\
{\bf s} & original published data & public \\
{\bf x} & additional published data & public \\
{\bf q} & contributed data & public \\
{\bf u} & user preferred data & private \\
{\bf t} & user defined temporary data & private \\
{\bf t} & user defined temporary data & private \\
\hline
\end{tabular}
\end{center}
@ -274,14 +275,12 @@ complete atom typing, or when modified charges are required.
\begin{tabular}{p{15mm}p{12mm}l}
\hline\hline
Card & Format & Description \\ \hline
I-1-1 & a1 & \$ to identify the start of a fragment \\ % $ for emacs
I-1-2 & a10 & name of the fragment, the tenth character\\
& & N: identifies beginning of a chain\\
& & C: identifies end of a chain\\
& & blank: identifies chain fragment\\
& & M: identifies an integral molecule\\
I-1-1 & a1 & \$ and \# for comments that describe the fragment \\ % $ for emacs
\hline
I-2-1 & i5 & number of atoms in the fragment\\
I-2-2 & i5 & number of parameter sets\\
I-2-3 & i5 & default parameter set\\
I-2-4 & i5 & number of z-matrix definition\\
\hline
\mc{3}{l}{For each atom one deck II} \\
\hline
@ -352,6 +351,7 @@ described in Tables \ref{tbl:nwaseg1}--\ref{tbl:nwaseg6}.
\begin{tabular*}{150mm}{p{15mm}p{12mm}l}
\hline\hline
Deck & Format & Description \\ \hline
I-0-1 & & \# lines at top are comments \\
I-1-1 & a1 & \$ to identify the start of a segment \\ %$ for emacs
I-1-2 & a10 & name of the segment, the tenth character\\
& & N: identifies beginning of a chain\\

4
doc/user/nwmd.tex
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@ -203,6 +203,8 @@ level & Description \\
{\bf s} & original published data \\
{\bf x} & additional published data \\
{\bf q} & contributed data \\
{\bf u} & user preferred data \\
{\bf t} & user defined temporary data\\
\hline
\end{tabular}
\end{center}
@ -1535,4 +1537,4 @@ batch <integer nfnewf>
\end{verbatim}
\end{description}
\end{description}

15
doc/user/prepare.tex
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@ -201,12 +201,15 @@ An example file \$HOME/.nwchemrc is:
\begin{verbatim}
ffield amber
amber_1 /soft/nwchem/share/amber/amber_s/amber99.par,spce.par
amber_2 /soft/nwchem/share/amber/amber_x/
amber_3 /usr/people/username/data/amber/amber_u/
spce /soft/nwchem/share/solvents/spce.rst
charmm_1 /soft/nwchem/share/charmm/charmm_s/
charmm_2 /soft/nwchem/share/charmm/charmm_x/
amber_1 /home/d3p852/nwchem/src/data/amber_s/
amber_2 /home/d3p852/nwchem/src/data/amber_x/amber.par,glycam.par
amber_3 /home/d3p852/nwchem/src/data/amber_q/
spce /home/d3p852/nwchem/src/data/solvents/spce.rst
thfs /home/d3p852/nwchem/src/data/solvents/thfs.rst
clfm /home/d3p852/nwchem/src/data/solvents/clfm.rst
meoh /home/d3p852/nwchem/src/data/solvents/meoh.rst
charmm_1 /home/d3p852/nwchem/src/data/charmm_s/charmm.par
charmm_2 /home/d3p852/nwchem/src/data/charmm_x/
\end{verbatim}
\section{System name and coordinate source}