#################### # QwikMD Input File # # # # # # # # # # #################### set QWIKMD::nucleicmcr {(not name QWIKMDDELETE and nucleic)} set QWIKMD::proteinmcr {(not name QWIKMDDELETE and protein)} set QWIKMD::heteromcr {(not name QWIKMDDELETE and hetero and not qwikmd_protein and not qwikmd_lipid and not qwikmd_nucleic and not qwikmd_glycan and not water or (resname ZZZ) )} set QWIKMD::glycanmcr {(not name QWIKMDDELETE and glycan)} set QWIKMD::lipidmcr {(not name QWIKMDDELETE and lipid)} atomselect macro qwikmd_protein $QWIKMD::proteinmcr atomselect macro qwikmd_nucleic $QWIKMD::nucleicmcr atomselect macro qwikmd_glycan $QWIKMD::glycanmcr atomselect macro qwikmd_lipid $QWIKMD::lipidmcr atomselect macro qwikmd_hetero $QWIKMD::heteromcr $QWIKMD::topGui.nbinput select 0 set QWIKMD::prepared 1 QWIKMD::changeMainTab $QWIKMD::topGui.nbinput.f1.nb select 0 QWIKMD::ChangeMdSmd 1 set aux "[file rootname $QWIKMD::basicGui(workdir,0)]" set QWIKMD::outPath ${aux} cd ${QWIKMD::outPath}/run/ set QWIKMD::inputstrct {bucf9rzln4-pqr-2X-fix195-460_QwikMD.psf bucf9rzln4-pqr-2X-fix195-460_QwikMD.pdb} QWIKMD::LoadButt {bucf9rzln4-pqr-2X-fix195-460_QwikMD.psf bucf9rzln4-pqr-2X-fix195-460_QwikMD.pdb} set QWIKMD::autorename 1 array set QWIKMD::basicGui {saltconc,MD,0 0.15 temperature,MDFF,0 27 scheme {VMD Classic} ambientocclusion off saltconc,SMD,0 0.15 live,0 1 live,1 0 currenttime,0 {Simulation time: 0.005 of 0.005 ns} currenttime,1 {} saltions,SMD,0 NaCl res Window plength 10.0 rendermode Normal saltions,MD,0 NaCl temperature,MD,0 27 solvent,SMD,0 Explicit mdPrec,0 2500 pspeed 2.5 temperature,SMD,0 27 mdtime,0 0.005 prtcl,SMD,smd 1 mdtime,1 4.0 material Opaque prtcl,MD,md 1 desktop white prtcl,MD,equi 1 solvent,MD,0 Explicit cuedensity 0.320000 prtcl,SMD,equi 1 shadows off quality Low saltions,MDFF,0 NaCl currenttime {Completed 0.000 of 0.000 ns} prtcl,MD,smd 0 prtcl,SMD,md 1 wsize {388 333} saltconc,MDFF,0 0.15 } array set QWIKMD::advGui {saltconc,MD,0 0.15 temperature,MDFF,0 27 scheme {VMD Classic} ambientocclusion off saltconc,SMD,0 0.15 live,0 1 live,1 0 currenttime,0 {Simulation time: 0.005 of 0.005 ns} currenttime,1 {} saltions,SMD,0 NaCl res Window plength 10.0 rendermode Normal saltions,MD,0 NaCl temperature,MD,0 27 solvent,SMD,0 Explicit mdPrec,0 2500 pspeed 2.5 temperature,SMD,0 27 mdtime,0 0.005 prtcl,SMD,smd 1 mdtime,1 4.0 material Opaque prtcl,MD,md 1 desktop white prtcl,MD,equi 1 solvent,MD,0 Explicit cuedensity 0.320000 prtcl,SMD,equi 1 shadows off quality Low saltions,MDFF,0 NaCl currenttime {Completed 0.000 of 0.000 ns} prtcl,MD,smd 0 prtcl,SMD,md 1 wsize {388 333} saltconc,MDFF,0 0.15 qmoptions,cmptcharge Off pntchrgopt,pcDist 10 protocoltb,MD,1,qmmm 0 protocoltb,MD,0,smd 0 live,0 1 protocoltb,QM/MM,2,saveAsTemplate 0 live,1 0 mdff,min 200 currenttime,0 {} analyze,advance,calcombo {H Bonds} currenttime,1 {} protocoltb,MD,1,lock 0 protocoltb,SMD,3,restrsel {} qmoptions,qmgentopo 0 analyze,advance,hbondsel2entry {Type Selection} res Window protocoltb,MD,1,restrsel {} rendermode Normal protocoltb,MD,3,saveAsTemplate 0 qmregopt,atmnumb 0 pspeed 2.5 protocoltb,SMD,2,saveAsTemplate 0 solvent,boxbuffer,SMD 15 prtcl,MD,md 1 qmoptions,ptcqmval {"!B3LYP 6-31G* Grid4 PAL[QWIKMD::procs]" "!EnGrad TightSCF"} protocoltb,QM/MM,3,qmmm 0 protocoltb,SMD,0,restrIndex {} protocoltb,QM/MM,2,smd 0 protocoltb,QM/MM,0,qmmm 0 protocoltb,QM/MM,3,lock 0 prtcl,SMD,md 1 saltions,MDFF,0 NaCl protocoltb,QM/MM,3,restrsel {} protocoltb,SMD,0,restrsel {} protocoltb,QM/MM,0,lock 0 ignoreforces 1 wsize {388 333} protocoltb,SMD,2,qmmm 0 protocoltb,QM/MM,0,restrIndex {} saltconc,MDFF,0 0.15 qmoptions,ptcharge On protocoltb,SMD,2,smd 0 membrane,xsize 30 protocoltb,SMD,1,restrIndex {} analyze,basic,selcombo backbone membrane,efect translate protocoltb,SMD,2,lock 0 protocoltb,MD,2,smd 0 protocoltb,MD,0,restrIndex {} saltions,SMD,0 NaCl solvent,QM/MM,0 Explicit solvent,boxbuffer,MDFF 15 protocoltb,QM/MM,1,saveAsTemplate 0 protocoltb,QM/MM,1,restrIndex {} solvent,boxbuffer,QM/MM 15 solvent,SMD,0 Explicit solvent,minimalbox,SMD 0 protocoltb,QM/MM,0,restrsel {} protocoltb,MD,3,qmmm 0 protocoltb,SMD,2,restrIndex {} protocoltb,MD,2,restrsel {} mdtime,0 0.005 analyze,basic,alicombo backbone mdtime,1 4.0 prtcl,SMD,smd 1 protocoltb,MD,0,qmmm 0 protocoltb,MD,2,saveAsTemplate 0 protocoltb,SMD,1,saveAsTemplate 0 membrane,axis x protocoltb,MD,3,lock 0 protocoltb,MD,0,lock 0 protocoltb,MD,1,restrIndex {} solvent,boxbuffer,MD 15 solvent,MDFF,0 Explicit analyze,advance,hbondsel1entry {Type Selection} saltions,QM/MM,0 NaCl protocoltb,QM/MM,2,restrIndex {} shadows off qmoptions,switchtype Switch protocoltb,SMD,3,restrIndex {} pntchrgopt,qmsolv 10 solvent,minimalbox,MDFF 0 analyze,basic,selentry {Type Selection} protocoltb,SMD,1,restrsel {} protocoltb,QM/MM,2,qmmm 0 protocoltb,MD,2,restrIndex {} saltconc,MD,0 0.15 protocoltb,MD,0 Minimization addmol 10 protocoltb,MD,1 Annealing protocoltb,MD,2 Equilibration protocoltb,MD,3 MD scheme {VMD Classic} protocoltb,QM/MM,2,lock 0 protocoltb,QM/MM,3,restrIndex {} protocoltb,QM/MM,1,smd 0 saltconc,SMD,0 0.15 protocoltb,SMD,1,qmmm 0 plength 10.0 protocoltb,SMD,0 Minimization protocoltb,SMD,1 Annealing saltions,MD,0 NaCl analyze,basic,alientry {Type Selection} protocoltb,SMD,2 Equilibration protocoltb,SMD,3 SMD protocoltb,MD,3,restrIndex {} temperature,SMD,0 27 protocoltb,SMD,1,lock 0 protocoltb,QM/MM,0,saveAsTemplate 0 protocoltb,SMD,1,smd 0 qmtable,QMreg 0 protocoltb,QM/MM,0 QMMM-Min protocoltb,QM/MM,1 QMMM-Ann protocoltb,QM/MM,1,restrsel {} protocoltb,QM/MM,2 QMMM-Equi solvent,minimalbox,QM/MM 0 protocoltb,QM/MM,3 QMMM protocoltb,MD,3,restrsel {} protocoltb,MD,1,saveAsTemplate 0 protocoltb,SMD,0,saveAsTemplate 0 prtcl,MD,equi 1 protocoltb,MD,1,smd 0 prtcl,SMD,equi 1 qmoptions,lssmode Off qmregopt,lblqmcharge 0 protocoltb,MD,2,qmmm 0 prtcl,MD,smd 0 currenttime {Completed 0.000 of 0.000 ns} protocoltb,MD,2,lock 0 temperature,MDFF,0 27 qmoptions,ressel {} protocoltb,QM/MM,3,saveAsTemplate 0 saltconc,QM/MM,0 0.15 protocoltb,SMD,2,restrsel {} membrane,multi 1 ambientocclusion off protocoltb,MD,0,restrsel {} protocoltb,QM/MM,3,smd 0 protocoltb,SMD,3,saveAsTemplate 0 protocoltb,QM/MM,1,qmmm 0 membrane,lipid POPC mdPrec,0 0 temperature,MD,0 27 protocoltb,QM/MM,1,lock 0 protocoltb,SMD,3,smd 0 membrane,ysize 30 desktop white protocoltb,SMD,3,qmmm 0 protocoltb,QM/MM,0,smd 0 protocoltb,SMD,0,qmmm 0 qmoptions,ptchrgschm Round protocoltb,QM/MM,2,restrsel {} qmoptions,soft ORCA analyze,basic,alicheck 0 solvent,MD,0 Explicit protocoltb,MD,0,saveAsTemplate 0 protocoltb,MD,3,smd 0 protocoltb,SMD,3,lock 0 cuedensity 0.320000 quality Low protocoltb,SMD,0,lock 0 solvent,minimalbox,MD 0 protocoltb,SMD,0,smd 0 mdff,mdff 50000 } array set QWIKMD::chains {2,2 {1 - 9261} 3,1 {I and hetero} 3,2 {1 - 475} 0,0 1 0,1 {A and protein} 1,0 1 0,2 {1 - 270} 1,1 {B and protein} 2,0 0 1,2 {271 - 534} 2,1 {W and water} 3,0 0} array set QWIKMD::index_cmb {{I and hetero,5} {chain "I" and qwikmd_hetero} {A and protein,1} NewCartoon {A and protein,2} {0 blue} {B and protein,1} NewCartoon {A and protein,3} 0 {B and protein,2} {1 red} {A and protein,4} rep1 {B and protein,3} 1 {A and protein,5} {chain "A" and qwikmd_protein} {B and protein,4} rep2 {W and water,5} {chain "W" and water} {B and protein,5} {chain "B" and qwikmd_protein} } set QWIKMD::delete {} array set QWIKMD::mutate {} array set QWIKMD::protonate { } set QWIKMD::mutindex {} set QWIKMD::protindex {} set QWIKMD::renameindex {} array set QWIKMD::dorename {} set QWIKMD::atmsRenameLog {} set QWIKMD::atmsReorderLog {} set QWIKMD::atmsDeleteLog {} set QWIKMD::patchestr {} set QWIKMD::state 0 set QWIKMD::load 1 set QWIKMD::prevconfFile {qwikmd_equilibration_0 qwikmd_production_1 qwikmd_production_2 qwikmd_production_3 qwikmd_production_4} set QWIKMD::confFile $QWIKMD::prevconfFile pbc box -center bb -color yellow -width 4 set QWIKMD::pbcInfo [pbc get -last end -nocheck] set QWIKMD::basicGui(live,0) 1 set QWIKMD::maxSteps {621000 2500 2500 2500 2500}