Geometry optimization three regions

scripting_documentation/RosettaScripts/multistage/GeometryOptimizationRosettaQM.md

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+# Geometry Optimization using RosettaQM
+
+## Summary
+In this tutorial, we are going to give an example of geometry optimization for a protein. 
+
+## Tutorial
+In this case, we have part of a zinc-finger protein. We want to optimize the geometry of protein:
+* in proximity of zinc, with quantum mechanics, 
+* its neighbourhood with a lower level of theory quantum mechanics, 
+* and the rest of protein with Rosetta's energy field. 
+
+<figure align="center">
+<img src="../../../images/GeometryOptimizationRosettaQM_image1.png" alt="drawing" width="200"/>
+<figcaption>Figure 1.</figcaption>
+</figure>
+
+Therefore, the protein will be seperated into three regions, which will be called reg1, reg2 and reg3, respectively. Then, different movers and scorings will be applied for each reigon. 
+
+Residue selectors ae used to specify each region.`reg1` is selected by residue numbers, and `reg2` is selected by `Neighborhood` selector. This selector compares the distance between beta carbons of selection (in this case, `reg1`) with beta carbons of other residues. If the distance is less than or equal to the threshold (in this case, 4A) it selects that residue. The `include_focus_in_subset="false"` tag means `reg2` excludes `reg1`. Figure 2. highights `reg1` with dark blue, and `reg2` with light blue. `reg3` is selected as anything not in `reg1` or `reg2` regions. 
+
+```
+<RESIDUE_SELECTORS>
+    <Index name="reg1" resnums="8,11,24,28,29"/>
+    <Neighborhood name="reg2" selector="reg1" distance="4.0" include_focus_in_subset="false" />
+    <Not name="reg3" selector="reg1,reg2">
+</RESIDUE_SELECTORS>
+```
+<figure align="center">
+<img src="../../../images/GeometryOptimizationRosettaQM_image2.png" alt="drawing" width="200"/>
+<figcaption>Figure 2.</figcaption>
+</figure>
+
+For each region, a different score function needs to be used. The following table gives a summary of that.
+
+| Region's name | Score function | 
+|-------------|----------------|
+| reg1 | |
+| reg2 | AM1. a semi-empirical score function|
+| reg3 | Rosetta ref2015 |
+
+
+```
+<SCOREFXNS>
+    <ScoreFunction name="ref2015" weights="ref2015_cart.wts"/>
+    <ScoreFunction name="qm_am1" weights="empty" >
+        <Reweight scoretype="gamess_qm_energy" weight="1.0" />
+        <Set
+            gamess_basis_set="AM1" 
+            gamess_use_smd_solvent="true"
+            gamess_use_scf_damping="false" 
+            gamess_max_scf_iterations="50"
+            gamess_electron_correlation_treatment="SE"
+            gamess_use_h_bond_length_constraints="true"
+            gamess_h_bond_length_constraint_force="10" 
+            />
+    </ScoreFunction>
+    <ScoreFunction name="qm_n21" weights="empty" >
+        <Reweight scoretype="gamess_qm_energy" weight="1.0" />
+        <Set 
+            gamess_basis_set="N21"
+            gamess_use_smd_solvent="true"
+            gamess_use_scf_damping="true"
+            gamess_max_scf_iterations="50"
+            gamess_electron_correlation_treatment="HF"
+            gamess_ngaussian="3" 
+            gamess_threads="4"
+            gamess_multiplicity="1"
+            gamess_npfunc="1" 
+            gamess_ndfunc="1"
+             />
+    </ScoreFunction>
+    <ScoreFunction name="qm_n21_hmo" weights="empty" >
+        <Reweight scoretype="gamess_qm_energy" weight="1.0" />
+        <Set 
+            gamess_basis_set="N21"
+            gamess_use_scf_damping="true"
+            gamess_max_scf_iterations="50"
+            gamess_electron_correlation_treatment="HF"
+            gamess_ngaussian="3" 
+            gamess_threads="4" 
+            gamess_multiplicity="1" 
+            gamess_fmo_calculation="true" 
+            gamess_hybrid_molecular_orbital="3-21G"
+            gamess_hybrid_molecular_orbital_file="<path-to-games>/gamess/tools/fmo/HMO/HMOs.txt"
+            gamess_max_fmo_monomer_scf_iterations="50"
+            />
+    </ScoreFunction>
+    <MultiScoreFunction name="multi_score_fxn" dump_pdbs="true" >
+        <SimpleCombinationRule />
+        <Region scorefxn="qm_am1" residue_selector="reg1" >
+            <CappedBondResolutionRule/>
+        </Region>
+        <Region scorefxn="qm_n21_hmo" residue_selector="reg2">
+            <CappedBondResolutionRule/>
+        </Region>
+        <Region scorefxn="r15" >
+            <CappedBondResolutionRule/>
+        </Region>
+    </MultiScoreFunction>
+
+</SCOREFsXNS>
+```
+
+```
+<SIMPLE_METRICS>
+    <TotalEnergyMetric 
+        name="gamess_point_energy_subset" 
+        scorefxn="multi_score_fxn" 
+        custom_type="E_QM_REGIONS_"
+    />
+</SIMPLE_METRICS>
+
+<MOVERS>
+    <GamessQMGeometryOptimizationMover 
+        name="qm_geo_opt_msfxn" 
+        gamess_threads="4" 
+        msfxn_name="multi_score_fxn" 
+        msfxn_classical_cartmin="true" 
+    />
+
+</MOVERS>
+
+<PROTOCOLS>
+    <Add mover="qm_geo_opt_msfxn"/>
+    <Add metrics="gamess_point_energy_subset"/>
+</PROTOCOLS>
+```