Unscaled bases are now fixed during initial minimization, should be more robust

CanonicalNucleotideAtoms.py

@@ -33,6 +33,7 @@ class CanonicalNucleotide():
         for k1,k2 in zip(('name','type'),('f1','f2')):
             self.props[k1] = [str(x,'utf-8') for x in d[k2]]
 
+        self.props['beta'] = np.ones(len(d['f1']))
         # self.props['name'] = [str(x) for x in d['f1']]
         # self.props['type'] = [str(x) for x in d['f2']]
 
@@ -82,6 +83,7 @@ class CanonicalNucleotide():
                     rvec = scale*(rvec-r0) + r0
                     for k,r in zip(('x','y','z'), rvec):
                         c.props[k][i] = r
+                    c.props["beta"][i] = 0
             else:
                 if self.sequence in ("A","G"):
                     i0 = self.index("N9")-1
@@ -94,6 +96,7 @@ class CanonicalNucleotide():
                         rvec = scale*(rvec-r0) + r0
                         for k,r in zip(('x','y','z'), rvec):
                             c.props[k][i] = r
+                        c.props["beta"][i] = 0
         
         return c
     

atomicModel.py

@@ -1409,7 +1409,14 @@ cellBasisVector3 0 0 1000
 
 if {$nLast == 0} {
     temperature 300
-    minimize 4800
+    fixedAtoms on
+    fixedAtomsForces on
+    fixedAtomsFile $prefix.pdb
+    fixedAtomsCol B
+    minimize 2400
+
+    fixedAtoms off
+    minimize 2400
 } else {
     bincoordinates  output/$prefix-$nLast.restart.coor
     binvelocities   output/$prefix-$nLast.restart.vel