Download File PES 2021 J. Bellingham Face By Sa...
DOWNLOAD ->->->-> https://ssurll.com/2tD4Ru
The natural extension of the ARM code has been to extend the general accuracy and applicability of the models and, most importantly, the level of automation in building protocol. Section 4 presents the advanced Automatic Rhodopsin Model building protocol (a-ARM), which meant completely rewriting the previous ARM code, and incorporating the possibility to automatically prepare inputs for the protocol itself. The completely new input preparation phase removed the need for user files manipulation and possible source of errors, hence achieving reliability and complete reproducibility of the results. The code behind a-ARM has also been used to power a web-interface, which allows, in principle, any user to obtain rhodopsin models of the same quality (Web-ARM, Sect. 5). This meant the extension of the benchmarking pool to more rhodopsins, thus increasing the applicability of the protocol, which, in turn, made it possible to use ARM models to guide the rational design of rhodopsins. More specifically, a-ARM can now be used to suggest which residue to mutate to obtain, for instance, a desired spectroscopic effect.
Overview of the most relevant features of the input file generator, introduced in the \\({a}\\text {-ARM}\\) version of the protocol. Methodological and automation improvements achieved with the input file generator, in terms of: initial setup; automatic strategy adopted for the assignment of protonation states for ionizable residues; replacement of the software (i.e., fpocket instead of CASTp) for the automatic generation of the chromophore cavity; automatic approach to define the charge of the \\(\\text{IS}\\) and \\(\\text{OS}\\) surfaces and automatic counterion placement based on energy minimization
In order to generate an \\(\\text{ARM QM/MM model}\\), \\(\\text{Web-ARM}\\) goes through the four phases explained in Section 2.1 of Ref. [74], and illustrated in Fig. 13. As described for the command-line version, the procedure starts with the initial structure of the rhodopsin variant and finishes with the generation of the \\(\\text {S}_{0}\\) equilibrium geometry along with the calculations on absorption properties. During such a procedure, the interface gives the user enough flexibility to generate either \\({a}\\text {-ARM}\\) \\(_\\text {default}\\) or \\({a}\\text {-ARM}\\) \\(_\\text {customized}\\) inputs (see Sect. 4.1), the former automatically and the latter by modifying some of the default choices. This is made on top of the implementation of the input file generator inside the framework of the web interface. Then, the so-generated \\(\\text{ARM input}\\) is used to compute a \\(\\text{QM/MM}\\) model, by using the QM/MM model generator. The \\(\\text{Web-ARM}\\) internal driver takes care of performing all the necessary steps, as well as submitting the calculations to the dedicated computational facilities.
One feature of the interface is that, once a \\(\\text{QM/MM}\\) model is generated, the user is provided with a summary of all the relevant data (i.e., energetics, oscillator strengths), along with a downloadable file (in compressed format) containing the major output files. Further information, and a complete walk-through, are provided in a Tutorial that can be accessed/downloaded from the \\(\\text{Web-ARM}\\) main web page. 781b155fdc