update features for ORCA6

bin/cmmde.py

@@ -129,6 +129,7 @@ parser.add_argument('-droplet','--droplet',type=str,default='False',help='Apakah
 parser.add_argument('-r_droplet','--droplet_radius',type=float,default=8.0, help='Radius droplet dalam Angstrom. Default: 10.0.')
 # DOCKER module in Orca 6
 parser.add_argument('-guest','--guest',type=str, default='none',help='File untuk docking menggunakan Orca.')
+parser.add_argument('-guestcharge','--guestcharge',type=int, default=0,help='Muatan molekul ligan/guest yang akan didocking. Default:0.')
 parser.add_argument('-docklevel','--docklevel',type=str,default='NORMAL', help='Tingkat akurasi docking. Default: NORMAL. Pilihan: SCREENING, COMPLETE.')
 parser.add_argument('-nrepeatguest','--nrepeatguest',type=int,default=1, help='Jumlah ligan yang akan dilibatkan dalam docking. Default: 1.')
 parser.add_argument('-cumulativeguest','--cumulativeguest',type=str,default='False',help='Update file ligan yang akan didocking. Default: False.')
@@ -288,7 +289,7 @@ elif ('.mol2' not in opt.input and '.xyz' not in opt.input and '.pdb' not in opt
     geom = 'geom.xyz'
 ### ORCA
 if opt.software == 'orca':
-    orca(opt.job,opt.method,opt.nproc,geom,opt.charge,opt.mult,opt.scalefreq,opt.temp,opt.pressure,opt.nroots,opt.tda,opt.solvent,opt.constraints,opt.qmatoms,opt.totalcharge,opt.totalmult,opt.qm2method,opt.qm2basis,opt.activeatoms,opt.hessfile,opt.dispersion,opt.aim,opt.produk,opt.transitionstate,opt.irciter,opt.printlevel, opt.inithess,opt.grid, opt.finalgrid,opt.iter,opt.solvtype,opt.cpcmsurface,opt.draco,opt.draco_charges,opt.solvator,opt.nsolv,opt.solventfile,opt.solvprint,opt.randomsolv,opt.fixsolute,opt.use_eeq,opt.droplet,opt.droplet_radius,opt.guest,opt.docklevel,opt.nrepeatguest,opt.cumulativeguest,opt.fixhost,opt.evpes,opt.nopt,opt.no_opt,opt.goat_iter,opt.goat_opt_iter,opt.skip_initopt,opt.randomseed,opt.readensemble,opt.autowall,opt.mintemplist,opt.nworkers,opt.maxitermult,opt.keepworker,opt.worker_randstart,opt.uphill_atoms,opt.gfn_uphill,opt.align,opt.en_diff,opt.max_en,opt.max_entropy,opt.conf_temp,opt.min_delta_S,opt.conf_degen,opt.free_heteroatoms,opt.free_nonh_atoms,opt.free_fragments,opt.freeze_bonds,opt.freeze_angles,opt.freeze_cistrans,opt.freeze_amides,opt.maxcoordnum,opt.max_topo_diff)
+    orca(opt.job,opt.method,opt.nproc,geom,opt.charge,opt.mult,opt.scalefreq,opt.temp,opt.pressure,opt.nroots,opt.tda,opt.solvent,opt.constraints,opt.qmatoms,opt.totalcharge,opt.totalmult,opt.qm2method,opt.qm2basis,opt.activeatoms,opt.hessfile,opt.dispersion,opt.aim,opt.produk,opt.transitionstate,opt.irciter,opt.printlevel, opt.inithess,opt.grid, opt.finalgrid,opt.iter,opt.solvtype,opt.cpcmsurface,opt.draco,opt.draco_charges,opt.solvator,opt.nsolv,opt.solventfile,opt.solvprint,opt.randomsolv,opt.fixsolute,opt.use_eeq,opt.droplet,opt.droplet_radius,opt.guest,opt.guestcharge,opt.docklevel,opt.nrepeatguest,opt.cumulativeguest,opt.fixhost,opt.evpes,opt.nopt,opt.no_opt,opt.goat_iter,opt.goat_opt_iter,opt.skip_initopt,opt.randomseed,opt.readensemble,opt.autowall,opt.mintemplist,opt.nworkers,opt.maxitermult,opt.keepworker,opt.worker_randstart,opt.uphill_atoms,opt.gfn_uphill,opt.align,opt.en_diff,opt.max_en,opt.max_entropy,opt.conf_temp,opt.min_delta_S,opt.conf_degen,opt.free_heteroatoms,opt.free_nonh_atoms,opt.free_fragments,opt.freeze_bonds,opt.freeze_angles,opt.freeze_cistrans,opt.freeze_amides,opt.maxcoordnum,opt.max_topo_diff)
 
 ### NWChem
 if opt.software == 'nwchem':

lib/cmmde_orca.py

@@ -1,4 +1,4 @@
-def orca(job,method,nproc,geom,charge,mult,scalfreq,temperature,pressure,nroots,tda,solvent,constraints,qmatoms,totalcharge,totalmult,qm2method,qm2basis,activeatoms,hessfile,disp,aim,product,ts,irciter, printlevel, inithess,grid, finalgrid,maxiter,solvtype,cpcmsurface,draco,draco_charges,solvator,nsolv,solventfile,solvprint,randomsolv,fixsolute,use_eeq,droplet,droplet_radius,guest,docklevel,nrepeatguest,cumulativeguest,fixhost,evpes,nopt,no_opt,goat_iter,goat_opt_iter,skip_initopt,randomseed,readensemble,autowall,mintemplist,nworkers,maxitermult,keepworker,worker_randstart,uphill_atoms,gfn_uphill,align,en_diff,max_en,max_entropy,conf_temp,min_delta_S,conf_degen,free_heteroatoms,free_nonh_atoms,free_fragments,freeze_bonds,freeze_angles,freeze_cistrans,freeze_amides,maxcoordnum,max_topo_diff):
+def orca(job,method,nproc,geom,charge,mult,scalfreq,temperature,pressure,nroots,tda,solvent,constraints,qmatoms,totalcharge,totalmult,qm2method,qm2basis,activeatoms,hessfile,disp,aim,product,ts,irciter, printlevel, inithess,grid, finalgrid,maxiter,solvtype,cpcmsurface,draco,draco_charges,solvator,nsolv,solventfile,solvprint,randomsolv,fixsolute,use_eeq,droplet,droplet_radius,guest,guestcharge,docklevel,nrepeatguest,cumulativeguest,fixhost,evpes,nopt,no_opt,goat_iter,goat_opt_iter,skip_initopt,randomseed,readensemble,autowall,mintemplist,nworkers,maxitermult,keepworker,worker_randstart,uphill_atoms,gfn_uphill,align,en_diff,max_en,max_entropy,conf_temp,min_delta_S,conf_degen,free_heteroatoms,free_nonh_atoms,free_fragments,freeze_bonds,freeze_angles,freeze_cistrans,freeze_amides,maxcoordnum,max_topo_diff):
     if 'opt' in job or 'Opt' in job or 'OPT' in job and not 'ts' in job: 
         method += ' opt'
     if 'freq' in job and ('XTB2' in method or 'XTB' in method):
@@ -19,11 +19,11 @@ def orca(job,method,nproc,geom,charge,mult,scalfreq,temperature,pressure,nroots,
         method += ' {}'.format(disp)
     if aim == 'true' or aim == 'True' or aim == 'TRUE':
         method += ' AIM'
-    if solvent != 'none' and ('XTB2' in method or 'XTB' in method or 'XTBFF' in method):
+    if solvent != 'none' and ('XTB2' in method or 'XTB' in method or 'XTBFF' in method or 'GFNFF' in method or 'GFN0XTB' in method or 'GFN1XTB' in method or 'GFN2XTB' in method):
         method += ' ALPB({})'.format(solvent)
         if solvtype == 'GBSA':
             method += ' GBSA({})'.format(solvent)
-    if solvent != 'none' and ('XTB2' not in method and 'XTB' not in method and 'XTBFF' not in method):
+    if solvent != 'none' and ('XTB2' not in method and 'XTB' not in method and 'XTBFF' not in method and 'GFNFF' not in method and 'GFN0XTB' not in method and 'GFN1XTB' not in method and 'GFN2XTB' not in method):
         if draco == True:
             method += ' DRACO'
         if solvtype == 'CPCM' or solvtype == 'cpcm':
@@ -143,6 +143,7 @@ end
         if 'docker' in job:
             print('%DOCKER',file=f)
             print("""  GUEST "{}" """.format(guest),file=f)
+            print('  GuestCharge {}'.format(guestcharge))
             print('  DOCKLEVEL {}'.format(docklevel),file=f)
             print('  NREPEATGUEST {}'.format(nrepeatguest),file=f)
             print('  CUMULATIVE {}'.format(cumulativeguest),file=f)