Merge pull request #71 from xixichennn/main

Update descriptions for normal and special ligand, and add OpenMMDL Analysis FAQ to docs/faq.rst

docs/faq.rst

@@ -30,3 +30,16 @@ In the case of a special ligand in the systems use the Amber Path and prepare th
 Can I use the CHARMM forcefield in the PDBFixer path for the simulations with my ligand?
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 No, currently only the Amber force fields are compatible with protein-ligand simulations.
+
+OpenMMDL Analysis
+------------------------------------
+
+How can I ensure that the residue numbering in the output files matches the original structure file for the convenience of post-MD analysis?
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+The '-ref' flag can be employed to align the residue numbers in the output topology file of the MD simulation with a reference protein.
+
+Why can't I get the PDB or PML file for the most occurring poses in the 'Binding_Modes_Markov_States' folder ?
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+The cause could be many. One possibility, as revealed by our internal testing, could be a problematic SDF file of the ligand. By default, **OpenMMDL Analysis** uses `obabel` to directly extract the ligand from the topology file of the MD trajectory and subsequently generate the ligand's SDF file. However, `obabel` may struggle to correctly process certain small molecules, such as charged molecules, as observed in our internal testing.
+
+A viable solution to this problem is to prepare the ligand SDF file using third party molecular tools such as MOE. Once prepared, the '-l' flag can be added to explicitly specify the correct SDF file for **OpenMMDL Analysis**.

docs/tutorial_amber_path.rst

@@ -109,7 +109,7 @@ Depends on the type of ligand the user intends to simulate, two options are avai
 
 2.1 **Normal Ligand**. 
 
-It refers to the small molecule that is made up of C, N, O, S, P, H, F, Cl, Br and I. The Amber files for the ligand will be generated using `Antechamber` and `Parmchk2`.
+It refers to the small molecule that is made up of C, N, O, S, P, H, F, Cl, Br and I, thus is compatible with GAFF and can be processed by `Antechamber` and `Parmchk2`.
 
 .. figure:: /_static/images/tutorials/Amber_Path/normalLigand.png
    :figwidth: 700px

openmmdl/openmmdl_setup/openmmdlsetup.py

@@ -400,7 +400,7 @@ def createAmberBashScript():
             "################################## Ligand ######################################"
         )
     if session["nmLig"]:
-        a_script.append("# Normal Ligand")
+        a_script.append("# Normal Ligand that is compatible with GAFF force field")
         nmLigFile = uploadedFiles["nmLigFile"][0][1]
         a_script.append(
             "nmLigFile=%s # the file name of ligand without suffix `.pdb` or `.sdf`"
@@ -444,7 +444,7 @@ def createAmberBashScript():
         )
 
     if session["spLig"]:
-        a_script.append("# Special Ligand")
+        a_script.append("# Special Ligand that is incompatible with GAFF force field")
         spLigFile = uploadedFiles["spLigFile"][0][1]
         a_script.append(
             "spLigFile=%s # the file name of ligand without suffix `.pdb`"

openmmdl/openmmdl_setup/templates/AmberOptions.html

@@ -193,7 +193,7 @@
           <!-- for normal ligand -->
           <div class="form-group">
             <label><input type="checkbox" name="nmLig" id="nmLig" oninput="optionChanged()" {{ 'checked' if session['nmLig'] else '' }}> Normal Ligand 
-              <span style="color:grey; font-weight: normal;">(refers to the chemical space is made up of C, N, O, S, P, H, F, Cl, Br and I)</span>
+              <span style="color:grey; font-weight: normal;">(Refers to the molecule whose chemical space is made up of C, N, O, S, P, H, F, Cl, Br and I, thus is compatible with GAFF)</span>
             </label>
           </div>
 
@@ -246,7 +246,7 @@
           <!-- for special ligand -->
           <div class="form-group">
             <label><input type="checkbox" name="spLig" id="spLig" oninput="optionChanged()" {{ 'checked' if session['spLig'] else '' }}> Special Ligand
-              <span style="color:grey; font-weight: normal;">(e.g. cofactor heme in CYP450 enzymes)</span>
+              <span style="color:grey; font-weight: normal;">(Refers to the ligand is not compatible with GAFF, e.g. cofactor heme in CYP450 enzymes)</span>
             </label>
 
           </div>

openmmdl/openmmdl_setup/templates/configureAmberFiles.html

@@ -45,7 +45,7 @@
     <!--normal ligand-->
     <div class="form-group" style="margin-left: 120px">
         <label><input type="checkbox" name="nmLig" id="nmLig" oninput="optionChanged()"> Normal Ligand 
-            <span style="color:grey; font-weight: normal;">(refers to the chemical space is made up of C, N, O, S, P, H, F, Cl, Br and I)</span>
+            <span style="color:grey; font-weight: normal;">(Refers to the ligand whose chemical space is made up of C, N, O, S, P, H, F, Cl, Br and I, thus is compatible with GAFF)</span>
         </label>
     </div>
 
@@ -61,7 +61,7 @@
     <!--special ligand-->
     <div class="form-group" style="margin-left: 120px">
         <label><input type="checkbox" name="spLig" id="spLig" oninput="optionChanged()"> Special Ligand
-            <span style="color:grey; font-weight: normal;">(e.g. cofactor heme in CYP450 enzymes)</span>
+            <span style="color:grey; font-weight: normal;">(Refers to the ligand is not compatible with GAFF, e.g. cofactor heme in CYP450 enzymes)</span>
         </label>
     </div>