File: README.html

package info (click to toggle)
apbs 1.0.0-2
  • links: PTS, VCS
  • area: main
  • in suites: lenny
  • size: 38,840 kB
  • ctags: 7,893
  • sloc: ansic: 44,537; xml: 21,399; sh: 20,613; fortran: 17,796; yacc: 2,922; python: 2,804; makefile: 567; lex: 294; sed: 205; java: 134; awk: 26
file content (141 lines) | stat: -rw-r--r-- 4,332 bytes parent folder | download | duplicates (3)
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
<html> 
	<head> 
		<title>APBS version validation and test cases</title> 
	</head>

	<body>
		<h1> APBS examples and test cases </h1>
		<i> $Id: README.html 1038 2006-12-29 22:01:25Z sobolevnrm $</i>

		<p> This directory serves as the root directory for the APBS test
		suite.  In each directory you will find example input files to use with
		APBS and a README file displaying the results for different versions of
		APBS. </p>

		<p> Executing <code>make test</code> in each directory will run the
		examples for that directory and log the results to
		<code>TESTRESULTS.log</code>.  Executing <code>make test</code> from
		the root examples directory will run all the tests listed below.  Tests
		will either pass, pass with rounding error (within 1E-9 of the expected
		result), or fail outright. </p>


		<ul>
			<li>Actin dimer (actin-dimer) 
			<ul> 
				<li><a href="actin-dimer/README.html">README</a> </li>
				<li>Source:  Dave Sept</li>
				<li>Description:  Calculate binding energies for actin dimers.
				This is an example of a large biomolecule binding energy
				calculation that often requires parallel focusing.</li>
			</ul> 
			</li>


			<li> Alkane nonpolar solvation energies (alkanes) 
			<ul>
				<li> <a href="alkanes/README.html">README</a> </li>
				<li> Source:  Nathan Baker, Jason Wagoner </li>
				<li> Description:  Calculate nonpolar solvation energies for various
				alkanes.  Taken from Wagoner JA, Baker NA. Assessing implicit models
				for nonpolar mean solvation forces: the importance of dispersion and
				volume terms. Proc Natl Acad Sci USA, 103, 8331-8336, 2006.
				<a
					href="http://dx.doi.org/10.1073/pnas.0600118103">(http://dx.doi.org/10.1073/pnas.0600118103)</a>
				</li>
			</ul>
			</li>

			<li> Born ion (born)
			<ul>
				<li><a href="born/README.html">README</a> </li>
				<li>Source:  Nathan Baker </li>
				<li>Description:  Calculate solvation energies for ions of
				various sizes and compare to the analytical results.</li>
			</ul>
			</li>

			<li>FKBP (FKBP)
			<ul>
				<li><a href="FKBP/README.html">README</a></li>
				<li>Source: Jung-Hsin Lin</li>
				<li>Description:  Binding of various (small) ligands to FKBP.  Analogous to
				HCA binding case (except it works).</li>
			</ul>
			</li>

			<li>HCA ligand binding (hca-bind)
			<ul>
				<li><a href="hca-bind/README.html">README</a></li>
				<li>Source:  UHBD </li>
				<li>Description:  Calculate the binding of a small molecule (acetazolamide)
				to a medium-sized protein (human carbonic anhydrase).</li>
			</ul>
			</li>

			<li>Acetic acid ionization (ionize)
			<ul>
				<li><a href="ionize/README.html">README</a></li>
				<li>Source: UHBD</li>
				<li>Description:  Calculate electrostatic contributions to the ionization
				energy of acetic acid.</li>
			</ul>
			</li>

			<li>Ion-ion PMF (ion-pmf)
			<ul>
				<li><a href="ion-pmf/README.html">README</a></li>
				<li>Source: Nathan Baker</li>
				<li>Description:  Calculate solvation energies and solvation force components
				for ion pairs.</li>
			</ul>
			</li>

			<li>Ion-protein interaction energies (ion-protein)
			<ul>
				<li><a href="ion-protein/README.html">README</a></li>
				<li>Source:  Dave Sept</li>
				<li>Description:  Calculate polar energy of placing an ion near a
				macromolecule</li>
			</ul>
			</li>

			<li>PKA-balanol binding (pka-lig)
			<ul>
				<li><a href="pka-lig/README.html">README</a></li>
				<li>Source:  Chung Wong</li>
				<li>Description:  Calculate binding energies of a ligand to protein kinase
				A.</li>
			</ul>
			</li>

			<li>Coulomb's law (point-pmf)
			<ul>
				<li><a href="point-pmf/README.html">README</a></li>
				<li>Source:  Nathan Baker</li>
				<li>Description:  See how well we do reproducing Coulomb's law.</li>
			</ul>
			</li>

			<li>Methanol solvation (solv)
			<ul>
				<li><a href="solv/README.html">README</a></li>
				<li>Source:  UHBD</li>
				<li>Description:  Calculate the solvation energies of methanol and
				methoxide.</li>
			</ul>
			</li>

			<li>Protein-RNA interactions (protein-rna)
			<ul>
				<li><a href="protein-rna/README.html">README</a></li>
				<li>Source:  David Draper</li>
				<li>Description:  Calculate the salt dependence of protein
				interactions with box B RNA hairpin.</li>
			</ul>
			</li>
		</ul>
		</p>

	</body>
</html>