From ad771196a6f4cb74a12b1c397e826ec8421fdf9c Mon Sep 17 00:00:00 2001 From: Aditya Wibawa Sakti Date: Fri, 16 Aug 2024 18:26:59 +0900 Subject: [PATCH] update features for ORCA6 --- bin/cmmde.py | 3 ++- lib/__pycache__/cmmde_orca.cpython-310.pyc | Bin 5783 -> 5923 bytes lib/cmmde_orca.py | 7 ++++--- 3 files changed, 6 insertions(+), 4 deletions(-) diff --git a/bin/cmmde.py b/bin/cmmde.py index 17043f8..8ddfef6 100755 --- a/bin/cmmde.py +++ b/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': diff --git a/lib/__pycache__/cmmde_orca.cpython-310.pyc b/lib/__pycache__/cmmde_orca.cpython-310.pyc index 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zO!%Gr+%kUg4E!hIQMY-bJ~XW$arfy{#J)r2}!wzQp( zA+JDoXbIwg?9+rgz2;xQrQtfY1DONqGRRes{hCnHtN#hv^Ki+$lio}88qfiqj-=}# z-3ECV1TU$gtNtFyL4&*xa>yVA(qoVXkY10-{5$*upuQ-6z4W%QNEYrO716 KUfRMY%w7N?tZH)r diff --git a/lib/cmmde_orca.py b/lib/cmmde_orca.py index e9f04a3..4b61c4c 100644 --- a/lib/cmmde_orca.py +++ b/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)