Step 2

The PKA system is simple enough that there is no need to split up the PDB model file from Step 1 into several pieces. The modified model file is:

        PDBModel PKA Simulation System - Chains A and I only.

        Chain A

        347
        LYS:8        ; GLY:9        ; SER:10       ; GLU:11       ; GLN:12       ; GLU:13       ; SER:14       ; VAL:15       ; LYS:16       ; GLU:17      
        PHE:18       ; LEU:19       ; ALA:20       ; LYS:21       ; ALA:22       ; LYS:23       ; GLU:24       ; ASP:25       ; PHE:26       ; LEU:27      
        LYS:28       ; LYS:29       ; TRP:30       ; GLU:31       ; ASN:32       ; PRO:33       ; ALA:34       ; GLN:35       ; ASN:36       ; THR:37      
        ALA:38       ; HIS:39       ; LEU:40       ; ASP:41       ; GLN:42       ; PHE:43       ; GLU:44       ; ARG:45       ; ILE:46       ; LYS:47      
        THR:48       ; LEU:49       ; GLY:50       ; THR:51       ; GLY:52       ; SER:53       ; PHE:54       ; GLY:55       ; ARG:56       ; VAL:57      
        MET:58       ; LEU:59       ; VAL:60       ; LYS:61       ; HIS:62       ; LYS:63       ; GLU:64       ; THR:65       ; GLY:66       ; ASN:67      
        HIS:68       ; PHE:69       ; ALA:70       ; MET:71       ; LYS:72       ; ILE:73       ; LEU:74       ; ASP:75       ; LYS:76       ; GLN:77      
        LYS:78       ; VAL:79       ; VAL:80       ; LYS:81       ; LEU:82       ; LYS:83       ; GLN:84       ; ILE:85       ; GLU:86       ; HIS:87      
        THR:88       ; LEU:89       ; ASN:90       ; GLU:91       ; LYS:92       ; ARG:93       ; ILE:94       ; LEU:95       ; GLN:96       ; ALA:97      
        VAL:98       ; ASN:99       ; PHE:100      ; PRO:101      ; PHE:102      ; LEU:103      ; VAL:104      ; LYS:105      ; LEU:106      ; GLU:107     
        TYR:108      ; SER:109      ; PHE:110      ; LYS:111      ; ASP:112      ; ASN:113      ; SER:114      ; ASN:115      ; LEU:116      ; TYR:117     
        MET:118      ; VAL:119      ; MET:120      ; GLU:121      ; TYR:122      ; VAL:123      ; PRO:124      ; GLY:125      ; GLY:126      ; GLU:127     
        MET:128      ; PHE:129      ; SER:130      ; HIS:131      ; LEU:132      ; ARG:133      ; ARG:134      ; ILE:135      ; GLY:136      ; ARG:137     
        PHE:138      ; SER:139      ; GLU:140      ; PRO:141      ; HIS:142      ; ALA:143      ; ARG:144      ; PHE:145      ; TYR:146      ; ALA:147     
        ALA:148      ; GLN:149      ; ILE:150      ; VAL:151      ; LEU:152      ; THR:153      ; PHE:154      ; GLU:155      ; TYR:156      ; LEU:157     
        HIS:158      ; SER:159      ; LEU:160      ; ASP:161      ; LEU:162      ; ILE:163      ; TYR:164      ; ARG:165      ; ASP:166      ; LEU:167     
        LYS:168      ; PRO:169      ; GLU:170      ; ASN:171      ; LEU:172      ; LEU:173      ; ILE:174      ; ASP:175      ; GLN:176      ; GLN:177     
        GLY:178      ; TYR:179      ; ILE:180      ; GLN:181      ; VAL:182      ; THR:183      ; ASP:184      ; PHE:185      ; GLY:186      ; PHE:187     
        ALA:188      ; LYS:189      ; ARG:190      ; VAL:191      ; LYS:192      ; GLY:193      ; ARG:194      ; THR:195      ; TRP:196      ; THR:197     
        LEU:198      ; CYS:199      ; GLY:200      ; THR:201      ; PRO:202      ; GLU:203      ; TYR:204      ; LEU:205      ; ALA:206      ; PRO:207     
        GLU:208      ; ILE:209      ; ILE:210      ; LEU:211      ; SER:212      ; LYS:213      ; GLY:214      ; TYR:215      ; ASN:216      ; LYS:217     
        ALA:218      ; VAL:219      ; ASP:220      ; TRP:221      ; TRP:222      ; ALA:223      ; LEU:224      ; GLY:225      ; VAL:226      ; LEU:227     
        ILE:228      ; TYR:229      ; GLU:230      ; MET:231      ; ALA:232      ; ALA:233      ; GLY:234      ; TYR:235      ; PRO:236      ; PRO:237     
        PHE:238      ; PHE:239      ; ALA:240      ; ASP:241      ; GLN:242      ; PRO:243      ; ILE:244      ; GLN:245      ; ILE:246      ; TYR:247     
        GLU:248      ; LYS:249      ; ILE:250      ; VAL:251      ; SER:252      ; GLY:253      ; LYS:254      ; VAL:255      ; ARG:256      ; PHE:257     
        PRO:258      ; SER:259      ; HIS:260      ; PHE:261      ; SER:262      ; SER:263      ; ASP:264      ; LEU:265      ; LYS:266      ; ASP:267     
        LEU:268      ; LEU:269      ; ARG:270      ; ASN:271      ; LEU:272      ; LEU:273      ; GLN:274      ; VAL:275      ; ASP:276      ; LEU:277     
        THR:278      ; LYS:279      ; ARG:280      ; PHE:281      ; GLY:282      ; ASN:283      ; LEU:284      ; LYS:285      ; ASP:286      ; GLY:287     
        VAL:288      ; ASN:289      ; ASP:290      ; ILE:291      ; LYS:292      ; ASN:293      ; HIS:294      ; LYS:295      ; TRP:296      ; PHE:297     
        ALA:298      ; THR:299      ; THR:300      ; ASP:301      ; TRP:302      ; ILE:303      ; ALA:304      ; ILE:305      ; TYR:306      ; GLN:307     
        ARG:308      ; LYS:309      ; VAL:310      ; GLU:311      ; ALA:312      ; PRO:313      ; PHE:314      ; ILE:315      ; PRO:316      ; LYS:317     
        PHE:318      ; LYS:319      ; GLY:320      ; PRO:321      ; GLY:322      ; ASP:323      ; THR:324      ; SER:325      ; ASN:326      ; PHE:327     
        ASP:328      ; ASP:329      ; TYR:330      ; GLU:331      ; GLU:332      ; GLU:333      ; GLU:334      ; ILE:335      ; ARG:336      ; VAL:337     
        SER:338      ; ILE:339      ; ASN:340      ; GLU:341      ; LYS:342      ; CYS:343      ; GLY:344      ; LYS:345      ; GLU:346      ; PHE:347     
        SER:348      ; GLU:349      ; PHE:350      ; PO3:197      ; ATP:400      ; MG:401       ; MG:402 

        Link              P::PO3:197::A        OG1::THR:197::A      PhosphorylatedThreonine

        LeftTermination   LYS:8
        RightTermination  PHE:350

        Variant           HIS:39               EpsilonProtonated
        Variant           HIS:62               EpsilonProtonated
        Variant           HIS:87               DoublyProtonated
        Variant           HIS:131              EpsilonProtonated
        Variant           HIS:294              EpsilonProtonated

        End

        Chain I

        20
        THR:1        ; THR:2        ; TYR:3        ; ALA:4        ; ASP:5        ; PHE:6        ; ILE:7        ; ALA:8        ; SER:9        ; GLY:10      
        ARG:11       ; THR:12       ; GLY:13       ; ARG:14       ; ARG:15       ; ASN:16       ; SER:17       ; ILE:18       ; HIS:19       ; ASP:20      

        LeftTermination   THR:1       
        RightTermination  ASP:20      

        Variant           HIS:19               EpsilonProtonated

        End

        Non-Chain Residues

        149
        HOH:500      ; HOH:501     
        HOH:502      ; HOH:504      ; HOH:505      ; HOH:506      ; HOH:507      ; HOH:508      ; HOH:509      ; HOH:510      ; HOH:512      ; HOH:513     
        HOH:514      ; HOH:515      ; HOH:516      ; HOH:518      ; HOH:519      ; HOH:520      ; HOH:521      ; HOH:522      ; HOH:523      ; HOH:524     
        HOH:525      ; HOH:526      ; HOH:527      ; HOH:528      ; HOH:530      ; HOH:531      ; HOH:532      ; HOH:533      ; HOH:534      ; HOH:535     
        HOH:536      ; HOH:537      ; HOH:538      ; HOH:539      ; HOH:540      ; HOH:541      ; HOH:542      ; HOH:543      ; HOH:544      ; HOH:545     
        HOH:546      ; HOH:547      ; HOH:548      ; HOH:549      ; HOH:550      ; HOH:551      ; HOH:552      ; HOH:553      ; HOH:554      ; HOH:555     
        HOH:556      ; HOH:557      ; HOH:558      ; HOH:559      ; HOH:560      ; HOH:561      ; HOH:562      ; HOH:563      ; HOH:564      ; HOH:565     
        HOH:566      ; HOH:567      ; HOH:569      ; HOH:570      ; HOH:571      ; HOH:573      ; HOH:574      ; HOH:575      ; HOH:576      ; HOH:577     
        HOH:578      ; HOH:579      ; HOH:580      ; HOH:581      ; HOH:582      ; HOH:583      ; HOH:584      ; HOH:585      ; HOH:587      ; HOH:588     
        HOH:589      ; HOH:590      ; HOH:591      ; HOH:592      ; HOH:593      ; HOH:594      ; HOH:597      ; HOH:598      ; HOH:600      ; HOH:601     
        HOH:602      ; HOH:604      ; HOH:607      ; HOH:608      ; HOH:609      ; HOH:610      ; HOH:612      ; HOH:613      ; HOH:614      ; HOH:616     
        HOH:617      ; HOH:618      ; HOH:619      ; HOH:620      ; HOH:621      ; HOH:622      ; HOH:623      ; HOH:625      ; HOH:626      ; HOH:628     
        HOH:629      ; HOH:630      ; HOH:632      ; HOH:633      ; HOH:634      ; HOH:635      ; HOH:636      ; HOH:637      ; HOH:638      ; HOH:639     
        HOH:640      ; HOH:641      ; HOH:642      ; HOH:643      ; HOH:644      ; HOH:645      ; HOH:646      ; HOH:647      ; HOH:649      ; HOH:650     
        HOH:651      ; HOH:652      ; HOH:653      ; HOH:654      ; HOH:655      ; HOH:656      ; HOH:657      ; HOH:658      ; HOH:659      ; HOH:660     
        HOH:661      ; HOH:662      ; HOH:663      ; HOH:664      ; HOH:665      ; HOH:667      ; HOH:668    

        End

        End

The file has the following features:

Only the A and I chains are being simulated and so the B and J chains have been removed.
The overall chain structure of the file has been retained except that the water residues in chain A have been moved into a Non-Chain Residues block. This block, which is nameless, can only occur once in a model file and is generally used to hold solvent and other molecules which are not properly part of chains.
In chain A, the MN residues have been renamed MG, ANP has become ATP, and MYR:403 has been removed as this is not relevant for the reaction.
In chain I, the inactive ALA:17 has been transformed into the active SER:17.
The Link statement in A remains except that its type has been changed to PhosphorylatedThreonine.
A number of Variant statements have been added to the A and I chain blocks. Variants modify the composition of a residue from its default state defined in pDynamo's PDB component library. In this case, all the variants specify alternative protonation states of histidine residues, the default state for which is the neutral, delta-protonated form. All other residues with variable protonation states take their default forms.
The LeftTermination and RightTermination statements remain the same as in the unedited model file. These terminations are, in fact, variants and so the type of termination can be specified after the residue information. This is not done here though and so default N-terminal (left) and C-terminal (right) terminations are chosen for the residues. A third type of termination is CyclicTermination. This is actually a link and indicates that the first and last residues in the chain should be bonded together.

A number of additional points are important:

The sequence information can be changed arbitrarily in the edited model file. However, it is generally convenient to keep the sequence specification as similar as possible to the old one. This helps to facilitate comparison with the original experimental structures but it is also easier because the mapping between the old and the new sequence specifications must be given when constructing the system. This is explained in more detail in Step 3.
Structures in some PDB files contain duplications of part of the sequence which are often indicated by the iCode parameter of the residue specification. All residues found in the PDB file are automatically included in the "raw" PDB model produced in Step 1 and so the unwanted iCodes (and other residues) should be removed when creating the new model file.
A protein (or other macromolecule) can have multiple protonation states, with significantly different properties, but the construction of a system requires that the exact atomic composition, including protonation pattern, be specified. Which one to choose?
There are a number of approaches. One is to analyze (or visualize) the geometry around each protonation site to see if there are hydrogen-bonding or other types of interaction that favour one protonation form over another. A second is to use one of the specially-developed algorithms for calculating macromolecular pKa values. Many of these are based upon the representation of the electrostatic interactions in a system by the Poisson-Boltzmann equation but some also employ empirical criteria. Links to a number of thirdparty tools of this type with web interfaces are listed here, but future releases of pDynamo should also have something similar.

Both approaches were used to decide on the protonation states of the histidine and other residues in the study of PKA. There was not much uncertainty in the choice in this instance, but in some cases there may be no alternative but to simulate systems with different protonation patterns.