Updated simulate.py to fix ENM name, copy force field

bin/enrgmd

@@ -64,7 +64,6 @@ http://dx.doi.org/10.1093/nar/gkw155
         model._clear_beads()
         model._generate_atomic_model(scale=args.backbone_scale)
         model.write_atomic_ENM( prefix )
-        model.atomic_simulate( output_name = prefix )
         try:
             shutil.copytree( get_resource_path("charmm36.nbfix"), "charmm36.nbfix" )
         except FileExistsError:
@@ -73,6 +72,7 @@ http://dx.doi.org/10.1093/nar/gkw155
             os.makedirs('output')
         except FileExistsError:
             ...
+        model.atomic_simulate( output_name = prefix )
         
     except:
         raise

mrdna/readers/cadnano_segments.py

@@ -9,6 +9,7 @@ from ..coords import readArbdCoords, readAvgArbdCoords
 from ..segmentmodel import SegmentModel, SingleStrandedSegment, DoubleStrandedSegment
 from ..model.dna_sequence import m13 as m13seq
 
+
 ## TODO: separate SegmentModel from ArbdModel so multiple parts can be combined
 ## TODO: catch circular strands in "get_5prime" cadnano calls
 ## TODO: handle special motifs

mrdna/simulate.py

 import os
 import tempfile
 from .coords import readArbdCoords, readAvgArbdCoords
+import shutil
+from . import get_resource_path
 
 arbd="/home/cmaffeo2/development/cuda/arbd.dbg/src/arbd" # reduced the mem footprint cause vmd
 namd="/home/cmaffeo2/development/namd-bin/NAMD_Git-2017-07-06_Linux-x86_64-multicore-CUDA/namd2"
@@ -97,7 +99,11 @@ def multiresolution_simulation( model, output_name,
         model.update_splines(coordinates)
         model._clear_beads()
         model._generate_atomic_model(scale=backbone_scale)
-        model.write_atomic_ENM( output_name )
+        try:
+            shutil.copytree( get_resource_path("charmm36.nbfix"), "charmm36.nbfix" )
+        except FileExistsError:
+            ...
+        model.write_atomic_ENM( output_prefix )
         model.atomic_simulate( output_name = output_prefix )
 
         ret = directory