README.md
1README for hca-bind APBS examples
2=================================
3
4The example input files in this directory calculate the binding of a small molecule (acetazolamide) to a medium-sized protein (human carbonic anhydrase).
5
6The UHBD calculations where performed using a van der Waals surface definition for the dielectric coefficient. This is simulated in the APBS input files by setting srad to 0.0.
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8Input File|Description|APBS Version|Results (kJ/mol)|UHBD (kJ/mol)
9---|---|---|---|---
10[apbs-mol.in](apbs-mol.in)|2-level focusing to 0.225 A, VdW surface, srfm mol|**1.5**|**-52.4648**|-70.00
11|||1.4.2|-52.4648
12|||1.4.1|-52.4648<sup>[6](#6)</sup>
13|||1.4|-51.4648<sup>[5](#5)</sup>
14|||1.3|-52.4647
15|||1.2.1|-52.4647
16|||1.2|-52.4647<sup>[4](#4)</sup>
17|||1.1.0|-52.4669
18|||1.0.0|-52.4669
19|||0.5.1|-52.4669<sup>[3](#3)</sup>
20|||0.5.0|-52.1062<sup>[2](#2)</sup>
21|||0.4.0|-52.4414
22[apbs-smol.in](apbs-smol.in)|2-level focusing to 0.225 A, VdW surface, srfm smol|**1.5**|**-54.0598**|-70.00
23|||1.4.2|-54.0598
24|||1.4.1|-54.0598
25|||1.3|-54.0598
26|||1.2.1|-54.0598
27|||1.2|-54.0598<sup>[4](#4)</sup>
28|||1.1.0|-54.0587
29|||1.0.0|-54.0587
30|||0.5.1|-54.0587<sup>[3](#3)</sup>
31|||0.5.0|-54.7039<sup>[2](#2)</sup>
32|||0.4.0|-54.0393<sup>[1](#1)</sup>
33|||0.3.2|-57.1192
34|||0.3.1|-57.1192
35|||0.3.0|-57.1192
36|||0.2.6|-57.1192
37|||0.2.5|-57.1192
38|||0.2.4|-57.1192
39|||0.2.3|-57.1123
40|||0.2.2|-57.1123
41|||0.2.1|-57.112
42|||0.2.0|-57.711
43|||0.1.8|-58.51
44
45<a name=1></a><sup>1</sup> The discrepancy in values between versions 0.4.0 and 0.3.2 is most likely due to three factors:
46
47- A bug fix in Vacc\_molAcc which removed spurious regions of high internal dielectric values
48- A switch in the algorithm used to compute the dielectric smoothing for srfm smol
49- The addition of the Vacc sphere density (sdens keyword) as a variable and a change in the default sdens value from 3.0 to 10.0
50
51<a name=2></a><sup>2</sup> The discrepancy in values between versions 0.5.0 and 0.4.0 is most likely due to the following factor(s):
52
53- A change in the autofocusing routine for APBS
54
55<a name=3></a><sup>3</sup> The discrepancy in values between versions 0.5.1 and 0.5.0 is most likely due to the following factor(s):
56
57- Bug fix regarding multipole behavior for neutral proteins
58
59<a name=4></a><sup>4</sup> APBS 1.2 has switched the multigrid smoothing algorithm from standard Gauss-Seidel to Gauss-Seidel red/black in order to facilitate parallelization. This switch has caused small differences in individual calculation energies which, when combined to the final answer, create larger errors (up to 0.04%). These errors can be reduced by resetting the APBS error tolerance to 1e-9 or smaller values. For a more detailed explanation, please see the APBS FAQ, [here](http://www.poissonboltzmann.org/docs/apbs-faq/#sources error calculation).
60
61<a name=5></a><sup>5</sup> The discrepancy in values between versions 1.3 and 1.4 is most likely due to the following factor(s):
62
63- Translation of contrib/pmgZ library from FORTRAN to C
64- Differences in numerical implementations between FORTRAN and C compilers result in small round-off discrepencies
65- Small margins due to these round-off discrepencies acumulate in the computations
66
67<a name=6></a><sup>6</sup> The discrepancy in the result between versions 1.4 and 1.4.1-binary is most likely due to a reporting error.
68
69Please see the ChangeLog or the [APBS website](http://www.poissonboltzmann.org/) for more information.
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