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. 7 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. 70 71 72