From 9a698dab7976dd118347bfc537df488202ed8901 Mon Sep 17 00:00:00 2001
From: ISDementyev <65086972+ISDementyev@users.noreply.github.com>
Date: Tue, 14 Sep 2021 17:50:00 -0400
Subject: [PATCH 1/4] Made a few changes (to account for no constraints)

---
 utils.py | 9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

diff --git a/utils.py b/utils.py
index 6953298..8a6dc05 100644
--- a/utils.py
+++ b/utils.py
@@ -200,11 +200,12 @@ def buildPeptide(peptide, customAngles=False):
     :return:
     """
     geo = Geometry.geometry(peptide[0])
-    angles_to_constrain = findAngles()  # all values in the list are strings
-    printRecord("Found angles_to_constrain successfully, beginning to constrain...\n")
-    
+
     if customAngles:
         printRecord("customAngles on\n")
+        angles_to_constrain = findAngles()  # all values in the list are strings
+        printRecord("Found angles_to_constrain successfully, beginning to constrain...\n")
+        
         phis = {row[0]: float(row[1]) for row in angles_to_constrain}
         psis = {row[0]: float(row[2]) for row in angles_to_constrain}
         
@@ -212,6 +213,8 @@ def buildPeptide(peptide, customAngles=False):
             if int(row[0]) == 0:
                 printRecord('phi[0] and psi[0]:', phis[row[0]], psis[row[0]], "\n") # only used for debugging
                 geo.phi, geo.psi = phis[row[0]], psis[row[0]]
+    else:
+        printRecord("Custom angles off")
         
     structure = PeptideBuilder.initialize_res(peptide[0])
         

From 0233d128484c737a20f515f404119a9141b8b684 Mon Sep 17 00:00:00 2001
From: ISDementyev <65086972+ISDementyev@users.noreply.github.com>
Date: Thu, 23 Sep 2021 13:42:47 -0400
Subject: [PATCH 2/4] Added resi indexing issue

---
 README_CONSTRAINTS.md | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/README_CONSTRAINTS.md b/README_CONSTRAINTS.md
index cd303be..9557115 100644
--- a/README_CONSTRAINTS.md
+++ b/README_CONSTRAINTS.md
@@ -63,7 +63,7 @@ residue_num,phi,psi,chain_id
 5,-85,-120,0
 ```
 
-### Common errors that might occur
+### Common errors that might occur**
 *Assuming everything above is followed*, some common errors that might show up are:
 
 1. ```Particle Coordinate is nan```
@@ -86,4 +86,8 @@ Psi: [<AtomGroup with 4 atoms>, None]
 ```
 Which shows the problem mentioned earlier in this paragraph.
 
+3. Residue indexing issue
+
+In PDB files, whenever a new chain starts, the residue indexes start counting from 0. However, this is not the case with OpenMM. It will continue counting the residues. For instance, say a PDB contained a 2-chain protein with 10 residues each. In the ```.pdb``` file, once residue 10 of Chain A is reached, it will count residue 1 of Chain B. However, OpenMM will count residue 1 of Chain B as residue 11 (or rather, residue 10 by its counting convention). While this program has been written to account for such an error, it is always good to keep this in mind, especially when writing your own modifications to the simulation or analysis code.
+
 ****This is by no means an exhaustive list. If more errors are found, they will be added here.**

From 21ed42d01c9022f0cb6c1549ae0eaf261952c151 Mon Sep 17 00:00:00 2001
From: ISDementyev <65086972+ISDementyev@users.noreply.github.com>
Date: Fri, 8 Oct 2021 12:28:51 -0400
Subject: [PATCH 3/4] Added *.out files - not really necessary

---
 .gitignore | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.gitignore b/.gitignore
index 6e2ab84..39cbb64 100644
--- a/.gitignore
+++ b/.gitignore
@@ -6,3 +6,4 @@ old/resultsAnalysis.py
 testScripts/
 old/oldFunctions.py
 misc
+*.out

From 7b417b86f3c535e90bba32fea27d68dfeeecec3d Mon Sep 17 00:00:00 2001
From: ISDementyev <65086972+ISDementyev@users.noreply.github.com>
Date: Sun, 31 Oct 2021 23:32:59 -0400
Subject: [PATCH 4/4] Update main.py

---
 main.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/main.py b/main.py
index dce4695..319b011 100644
--- a/main.py
+++ b/main.py
@@ -94,6 +94,7 @@
     params['sequence'] = cmdLineInputs[1] # sequence specified from command line
     params['peptide'] = cmdLineInputs[2] # peptide specified from command line
     params['max walltime'] = cmdLineInputs[3] # maximum walltime
+    params['peptide backbone constraint constant'] = cmdLineInputs[4]
 elif params['device'] == 'local':
     params['run num'] = 0  # manual setting, for 0, do a fresh run, for != 0, pickup on a previous run.
     params['sequence'] = 'CCCGGGCCCGGG' # manually set sequence # ATP aptamer
@@ -167,7 +168,6 @@
 params['rigid water'] = True
 params['constraint tolerance'] = 1e-6
 params['hydrogen mass'] = 1.5  # in amu - we can increase the time if we increase this value
-params['peptide backbone constraint constant'] = 10000
 
 # paths
 if params['device'] == 'local':