debug

autosolvate/FFmetalcomplex.py

@@ -13,8 +13,8 @@
 
 
 class genFF():
-    def __init__(self, filename,metal_charge, chargefile, solvent,slv_count,folder,
-                 mode,spinmult,software,basisset,method,cubesize,closeness,
+    def __init__(self, filename,metal_charge, chargefile, solvent,slv_count,folder,maxcore,
+                 mode,spinmult,software,basisset,method,cubesize,closeness,cutoff,
                  totalcharge,nprocs,QMexe,amberhome,solvent_off,solvent_frcmod,opt):
         self.metal_charge = metal_charge
         self.filename = filename
@@ -37,6 +37,8 @@ def __init__(self, filename,metal_charge, chargefile, solvent,slv_count,folder,
         self.closeness = closeness
         self.slv_count = slv_count
         self.folder = folder
+        self.cutoff = cutoff
+        self.maxcore = maxcore
 
 
     def inputCheck(self):
@@ -465,23 +467,23 @@ def build(self):
 
         print('******************** start to generate inputs for MCPB.py -s 1 ********************')
         step1 = autoMCPB.AutoMCPB(filename=self.filename,metal_charge=self.metal_charge, spinmult=self.spinmult,amberhome=self.amberhome,
-                       mode=self.mode,chargefile=self.chargefile,round='1',software=self.software)
+                       mode=self.mode,chargefile=self.chargefile,round='1',software=self.software,cutoff=self.cutoff)
         step1.build()
 
         print('******************** Finish generating inputs for MCPB.py -s 1 ********************')
         print('******************** start to QM calculations for', self.software + '_small_opt', self.software + '_small_fc',self.software + '_large_mk','********************')
         step2 = QM_gen.QM_inputs_gen(filename=self.filename,software=self.software,caltype='opt',multi=self.spinmult,method=self.method,
-                            basisset=self.basisset,metal='default',totalcharge=self.totalcharge,nprocs=self.nprocs,opt=self.opt)
+                            basisset=self.basisset,metal='default',totalcharge=self.totalcharge,nprocs=self.nprocs,opt=self.opt,maxcore=self.maxcore)
        # print(self.filename,'!!!!!!!!!!!!!!!!')
         step2.build()
         self.runQM_opt()
         step3 = QM_gen.QM_inputs_gen(filename=self.filename,software=self.software,caltype='fc',multi=self.spinmult,method=self.method,
-                            basisset=self.basisset,metal='default',totalcharge=self.totalcharge,nprocs=self.nprocs,opt=self.opt)
+                            basisset=self.basisset,metal='default',totalcharge=self.totalcharge,nprocs=self.nprocs,opt=self.opt,maxcore=self.maxcore)
         step3.build()
         self.runQM_freq()
 
         step4 = QM_gen.QM_inputs_gen(filename=self.filename,software=self.software,caltype='mk',multi=self.spinmult,method=self.method,
-                            basisset=self.basisset,metal='default',totalcharge=self.totalcharge,nprocs=self.nprocs,opt=self.opt)
+                            basisset=self.basisset,metal='default',totalcharge=self.totalcharge,nprocs=self.nprocs,opt=self.opt,maxcore=self.maxcore)
         step4.build()
         #print('#######################')
         self.runQM_mk()
@@ -497,7 +499,7 @@ def build(self):
 
         if checkfreq == 'converged':
             step5=autoMCPB.AutoMCPB(filename=self.filename,metal_charge=self.metal_charge, spinmult=self.spinmult,amberhome=self.amberhome,
-                        mode=self.mode,chargefile=self.chargefile,round='2',software=self.software)
+                        mode=self.mode,chargefile=self.chargefile,round='2',software=self.software,cutoff=self.cutoff)
             step5.build()
         #    print('nnnnnnnnnnnnnn')
         elif checkfreq == 'notconverged':
@@ -514,7 +516,7 @@ def build(self):
         if checkmk == 'converged':
             if self.software != 'orca':
                 step6 = autoMCPB.AutoMCPB(filename=self.filename,metal_charge=self.metal_charge, spinmult=self.spinmult,
-                mode=self.mode,chargefile=self.chargefile,round='3',software=self.software,amberhome=self.amberhome)
+                mode=self.mode,chargefile=self.chargefile,round='3',software=self.software,amberhome=self.amberhome,cutoff=self.cutoff)
                 step6.build()
             else:
                 if self.opt == 'Y':
@@ -557,14 +559,14 @@ def build(self):
             raise TypeError('Erorr: charge calculation is not finished!')
             sys.exit()
         if os.path.exists('resp2.chg'):
-            step7 = autoMCPB.AutoMCPB(filename=self.filename,metal_charge=self.metal_charge, spinmult=self.spinmult,
+            step7 = autoMCPB.AutoMCPB(filename=self.filename,metal_charge=self.metal_charge, spinmult=self.spinmult,cutoff=self.cutoff,
                         mode=self.mode,chargefile=self.chargefile,round='4',software=self.software,amberhome=self.amberhome)
             step7.build()
         else:
             raise TypeError('Erorr: can not find resp2.chg')
             sys.exit()
         if os.path.exists(self.filename + '_dry.prmtop'):
-            step8 = autoMCPB.AutoMCPB(filename=self.filename,metal_charge=self.metal_charge, spinmult=self.spinmult,
+            step8 = autoMCPB.AutoMCPB(filename=self.filename,metal_charge=self.metal_charge, spinmult=self.spinmult,cutoff=self.cutoff,
                         mode=self.mode,chargefile=self.chargefile,round='5',software=self.software,amberhome=self.amberhome)
             step8.build()
         else:
@@ -626,9 +628,9 @@ def build(self):
 """
 
 def startFFgen(argumentList):
-    options = 'hm:k:u:v:f:e:c:y:d:i:l:p:j:a:w:s:b:t:D:'
-    long_options = ["help", 'filename=', 'metal_charge=', 'spin=', 'mode=', 'folder=', 'rundir=',
-                'chargefile=', 'charge=', 'nprocs=', 'method=', 'cubesize=', 'closeness=', 'qmdir=',
+    options = 'hm:k:u:v:f:e:c:y:d:i:l:p:j:a:w:s:b:t:D:x:g:'
+    long_options = ["help", 'filename=', 'metal_charge=', 'spin=', 'mode=', 'folder=', 'rundir=','cutoff='
+                'chargefile=', 'charge=', 'nprocs=', 'method=', 'cubesize=', 'closeness=', 'qmdir=', 'maxcore='
                 'qmexe=', 'basisset=', 'solventoff=', 'solventfrcmod=', 'amberhome=', 'opt=', 'solvent=']
     arguments, values = getopt.getopt(argumentList, options, long_options)
     filename = None
@@ -653,7 +655,8 @@ def startFFgen(argumentList):
     cubesize = 54
     slv_count = 210*8
     folder = './'
-
+    cutoff = 2.8
+    maxcore = "1000"
 
     for currentArgument, currentValue in arguments:
         if currentArgument in ("-h", "--help"):
@@ -680,7 +683,9 @@ def startFFgen(argumentList):
                 -s  --solvent           name of solvent (water, methanol, chloroform, nma, acetonitrile)
                 -b  --cubesize          size of solvent cube in angstroms default: 54 
                 -t  --closeness         Solute-solvent closeness setting default value is used if the option is not specified
-                -D, --rundir            running directory where temporary files are stored, default: the current folder './'
+                -D  --rundir            running directory where temporary files are stored, default: the current folder './'
+                -x  --cutoff            the cutoff to defined bonded pair in MCPB default: 2.8
+                -g  --maxcore           the memory(M) requrested for orca calculation
 
 
                 '''
@@ -724,10 +729,15 @@ def startFFgen(argumentList):
             closeness = str(currentValue)
         elif currentArgument in ('-D','--rundir'):
             folder = str(currentValue)
+        elif currentArgument in ('-x','--cutoff'):
+            cutoff = str(currentValue)
+        elif currentArgument in ('-g','--maxcore'):
+            maxcore = str(currentValue)
+          #  print('cutoff=',cutoff)
 
 
-    builder = genFF(filename=filename,metal_charge=metal_charge, spinmult=spinmult,basisset=basisset,closeness=closeness,folder = folder,
-                    mode=mode,chargefile=chargefile,software=software,solvent_frcmod=solvent_frcmod,amberhome=amberhome,cubesize=cubesize,
+    builder = genFF(filename=filename,metal_charge=metal_charge, spinmult=spinmult,basisset=basisset,closeness=closeness,folder = folder,cutoff= cutoff,
+                    mode=mode,chargefile=chargefile,software=software,solvent_frcmod=solvent_frcmod,amberhome=amberhome,cubesize=cubesize,maxcore= maxcore,
                     totalcharge=totalcharge,nprocs=nprocs,QMexe=QMexe,method=method,solvent_off=solvent_off,opt=opt,solvent=solvent,slv_count=slv_count)
 
     builder.build()

autosolvate/QM_gen.py

@@ -10,7 +10,7 @@
 
 metalbasisset = ['LANL2DZ','SBKJC']
 vdw = {"H":1.1,"Li":2.2,"Be":1.9,"B":1.8,"C":1.7,"N":1.55,"O":1.52,"F":1.47,"Na":2.4,"Mg":2.2,"Al":2.1,"Si":2.1,
-        "P":1.8,"S":1.8,"Cl":1.75,"K":2.8,"Ca":2.31,"Sc":2.3,"Ti":2.15,"V":2.05,
+        "P":1.8,"S":1.8,"Cl":1.75,"K":2.8,"Ca":2.31,"Sc":2.3,"Ti":2.15,"V":2.05,"Pb":2.02,
         "Cr":2.05,"Mn":2.05,"Fe":2.05,"Co":2.0,"Ni":2.0,"Cu":2.0,"Zn":2.1,"Ga":2.1,
         "As":2.05,"Se":1.9,"Br":1.83,"Rb":2.9,"Sr":2.55,"Y":2.4,"Zr":2.3,"Nb":2.15,
         "Mo":2.1,"Tc":2.05,"Ru":2.05,"Rh":2.0,"Pd":2.05,"Ag":2.1,"Cd":2.2,"In":2.2,"I":1.98,"W":2.1,"Os":2.1,"Ir":2.1}
@@ -117,7 +117,7 @@ def get_crds_from_orcaopt(orcaout,trjxyz):
 
 
 class QM_inputs_gen():
-    def __init__(self, filename,software,caltype,multi,method,basisset,totalcharge,metal,nprocs,opt):
+    def __init__(self, filename,software,caltype,multi,method,basisset,totalcharge,metal,nprocs,opt,maxcore):
         self.software = software
         self.caltype = caltype
         self.multi = multi
@@ -129,6 +129,7 @@ def __init__(self, filename,software,caltype,multi,method,basisset,totalcharge,m
         self.metal = metal
         self.nprocs = nprocs
         self.opt = opt
+        self.maxcore = maxcore
 
         if self.totalcharge in ['default','Default'] :
             with open(self.info, 'r') as f:
@@ -255,6 +256,7 @@ def write_orca_opt(self,crds,out,multi,totalcharge,nprocs,basisset,method):
         ofile.write('! ' + method + ' ' + basisset + ' OPT\n')
         ofile.write('\n')
         ofile.write("%pal\nnprocs " + str(nprocs) + "\nend\n\n")
+        ofile.write('%maxcore ' + self.maxcore + '\n\n')
         ofile.write('* xyz ' + str(totalcharge) + ' ' + str(multi) + '\n')
         for line in crds:
             atomname = line[0]
@@ -269,6 +271,7 @@ def write_orca_fc(self,crds,out,multi,totalcharge,nprocs,basisset,method):
         ofile = open(out,'w')
         ofile.write('! ' + method + ' ' + basisset + ' Freq\n\n')
         ofile.write("%pal\nnprocs " + str(nprocs) + "\nend\n\n")
+        ofile.write('%maxcore ' + self.maxcore + '\n\n')
         ofile.write('* xyz ' + str(totalcharge) + ' ' + str(multi) + '\n')
         for line in crds:
             atomname = line[0]
@@ -283,6 +286,7 @@ def write_orca_mk(self,crds,out,multi,totalcharge,basisset,nprocs, method):
         ofile = open(out,'w')
         ofile.write('! ' + method + ' ' + basisset + ' keepdens\n\n')
         ofile.write("%pal\nnprocs " + str(nprocs) + "\nend\n\n")
+        ofile.write('%maxcore ' + self.maxcore + '\n\n')
         ofile.write('* xyz ' + str(totalcharge) + ' ' + str(multi) + '\n')
         for line in crds:
             atomname = line[0]

autosolvate/autoMCPB.py

@@ -162,7 +162,7 @@ class AutoMCPB():
 
     
     """
-    def __init__(self, filename, metal_charge, chargefile,mode,spinmult,round,software,amberhome): #liglist='', denticity='',ligcons='',atomsinfo='',ligand_charge='',metal_name=''):
+    def __init__(self, filename, metal_charge, chargefile,mode,spinmult,round,software,amberhome,cutoff): #liglist='', denticity='',ligcons='',atomsinfo='',ligand_charge='',metal_name=''):
         self.metal_charge = metal_charge
         self.filename = filename
         self.xyzfile = filename + '.xyz'
@@ -172,6 +172,7 @@ def __init__(self, filename, metal_charge, chargefile,mode,spinmult,round,softwa
         self.round = round
         self.software = software
         self.amberhome = amberhome
+        self.cutoff = cutoff
 
     def coordinates_reader_xyz(self):
         r"""
@@ -765,7 +766,7 @@ def generate_MCPB_input(self):
             f.write('software_version ' + self.software +'\n')
             f.write(original_pdb + '\n')
             f.write('group_name ' + self.filename + '\n')
-            f.write('cutoff 2.8\n')
+            f.write('cut_off ' + str(self.cutoff) + '\n')
             f.write(ion_ids + '\n')
             if self.ligcons != 'NA':
                 f.write(self.add_bonded_pairs + '\n')
@@ -1322,8 +1323,8 @@ def build(self):
                 self.checkingFF()
 
 def startautoMCPB(argumentList):
-    options = "hn:c:u:m:f:s:x:A:"
-    long_options = ["help",'filename=','metal_charge=','spin=','mode=','chargefile=','round=','software=','amberhome=']
+    options = "hn:c:u:m:f:s:x:A:e"
+    long_options = ["help",'filename=','metal_charge=','spin=','mode=','chargefile=','round=','software=','amberhome=','cutoff=']
     arguments, values = getopt.getopt(argumentList,options,long_options)
     filename = None
     metal_charge = None
@@ -1333,6 +1334,7 @@ def startautoMCPB(argumentList):
     software = 'gms'
     round = '1'
     amberhome = '$AMBERHOME/bin/'
+    cutoff = '2.8'
    # print(arguments)
     for currentArgument, currentValue in arguments:
         if currentArgument in ("-h", "--help"):
@@ -1348,7 +1350,8 @@ def startautoMCPB(argumentList):
                                         LG1 -1 # ligand name charge 
                 -s, --round             round of MCPB.py
                 -x, --software            g09,g16 or gms
-                -A, --amberhome         path of AmberTools bin 
+                -A, --amberhome         path of AmberTools bin
+                -e  --cutoff            cutoff of MCPB 
                 '''
             print(message)
             sys.exit()
@@ -1370,9 +1373,12 @@ def startautoMCPB(argumentList):
             software = str(currentValue)
         elif currentArgument in ('-A','--amberhome'):
             amberhome = str(currentValue)
+        elif currentArgument in ('-e','--cutoff'):
+            cutoff = str(currentValue)
 
 
-    builder = AutoMCPB(filename=filename,metal_charge=metal_charge, spinmult=spinmult,
+
+    builder = AutoMCPB(filename=filename,metal_charge=metal_charge, spinmult=spinmult,cutoff=cutoff,
                        mode=mode,chargefile=chargefile,round=round,software=software,amberhome=amberhome)
 
     builder.build()

autosolvate/boxgen_metal.py

@@ -41,8 +41,8 @@ def __init__(self, pdb_prefix, totalcharge,
         self.solvent_frcmod=solvent_frcmod
         self.solvent_off = solvent_off
         self.cube_size = cube_size
-        self.slu_pos = self.cube_size/2.0
-        self.pbcbox_size = self.cube_size+2
+        self.slu_pos = str(float(self.cube_size)/2.0)
+        self.pbcbox_size = str(float(self.cube_size)+2)
         self.amberhome = amberhome
         self.closeness = closeness
 
@@ -64,7 +64,7 @@ def __init__(self, pdb_prefix, totalcharge,
             self.closeness = 0.5
         self.waterbox_size = 8.0
         self.cube_size = cube_size
-        self.volumne = (self.cube_size * 10**(-10))**3
+        self.volumne = (float(self.cube_size) * 10**(-10))**3
         if self.solvent not in ['acetonitrile','water','methanol','nma','chloroform']:
             print("Warning: solvent not supported for automated counting determination, using the default number")
             slv_count = 210*8