#################### # QwikMD Input File # # # # # # # # # # #################### set QWIKMD::nucleicmcr {(not name QWIKMDDELETE and nucleic) and not (resid "216" and chain "A")} set QWIKMD::proteinmcr {(not name QWIKMDDELETE and protein or (resname LYR)) or (resid "300" and chain "A") or (resid "216" and chain "A")} 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) and not (resid "300" and chain "A") and not (resid "216" and chain "A")} set QWIKMD::glycanmcr {(not name QWIKMDDELETE and glycan) and not (resid "216" and chain "A")} set QWIKMD::lipidmcr {(not name QWIKMDDELETE and lipid) and not (resid "216" and chain "A")} 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 1 set QWIKMD::prepared 1 QWIKMD::changeMainTab $QWIKMD::topGui.nbinput.f2.nb select 0 QWIKMD::ChangeMdSmd 2 set aux "[file rootname $QWIKMD::basicGui(workdir,0)]" set QWIKMD::outPath ${aux} cd ${QWIKMD::outPath}/run/ set QWIKMD::inputstrct {1qhj_membrane_QwikMD.psf 1qhj_membrane_QwikMD.pdb} QWIKMD::LoadButt {1qhj_membrane_QwikMD.psf 1qhj_membrane_QwikMD.pdb} array set QWIKMD::basicGui {live 0 currenttime {Completed 0.000 of 0.000 ns} plength 10.0 desktop {} temperature,0 27 temperature,1 27 saltconc,0 0.15 scheme {VMD Classic} mdPrec,0 0 pspeed 2.5 saltions,0 NaCl mdtime,0 10.0 mdtime,1 4.0 currenttime,0 {} currenttime,1 {} solvent,0 Implicit } array set QWIKMD::advGui {live 0 currenttime {Completed 0.000 of 0.000 ns} plength 10.0 desktop {} temperature,0 27 temperature,1 27 saltconc,0 0.15 scheme {VMD Classic} mdPrec,0 0 pspeed 2.5 saltions,0 NaCl mdtime,0 10.0 mdtime,1 4.0 currenttime,0 {} currenttime,1 {} solvent,0 Implicit protocoltb,template MD.1 addmol 10 protocoltb,SMD,1,restrIndex {} protocoltb,MD,0 Minimization protocoltb,MD,6,saveAsTemplate 0 membrane,efect translate protocoltb,MD,1 Annealing analyze,basic,selcombo backbone protocoltb,SMD,2,lock 0 protocoltb,MD,2 Equilibration protocoltb,MD,3 MD protocoltb,MD,7,lock 1 protocoltb,MD,4 MD.1 protocoltb,MD,5 MD.2 membrane,multi 1 protocoltb,SMD,2,restrsel {} protocoltb,MD,6 MD.3 protocoltb,MD,7,restrsel {} protocoltb,MD,7 MD.4 protocoltb,MD,5,saveAsTemplate 0 protocoltb,MD,0,smd 0 protocoltb,MD,0,restrsel {} protocoltb,MD,5,restrIndex {} protocoltb,MD,4,lock 1 protocoltb,MD,2,smd 0 protocoltb,MD,4,smd 0 mdff,min 200 protocoltb,MD,0,restrIndex {} analyze,advance,calcombo {H Bonds} protocoltb,MD,6,smd 0 protocoltb,SMD,3,restrsel {} protocoltb,MD,1,lock 0 protocoltb,MD,4,saveAsTemplate 0 membrane,center,x 16.58989715576172 membrane,zmin -14.10213041305542 membrane,center,y 40.857994079589844 analyze,advance,hbondsel2entry {Type Selection} membrane,center,z 5.39786958694458 protocoltb,SMD,3,saveAsTemplate 0 protocoltb,MD,1,restrsel {} solvent,boxbuffer 15 membrane,zmax 24.89786958694458 membrane,boxedges {{-33.41010284423828 -9.142005920410156 -14.10213041305542} {-33.41010284423828 -9.142005920410156 24.89786958694458} {-33.41010284423828 90.85799407958984 24.89786958694458} {66.58989715576172 90.85799407958984 24.89786958694458} {-33.41010284423828 90.85799407958984 -14.10213041305542} {66.58989715576172 -9.142005920410156 -14.10213041305542} {66.58989715576172 90.85799407958984 -14.10213041305542} {66.58989715576172 -9.142005920410156 24.89786958694458}} protocoltb,SMD,0 Minimization membrane,lipid POPC protocoltb,SMD,1 Annealing protocoltb,SMD,2 Equilibration analyze,basic,alientry {Type Selection} protocoltb,SMD,3 SMD protocoltb,MD,3,saveAsTemplate 0 protocoltb,MD,3,restrIndex {} protocoltb,SMD,2,saveAsTemplate 0 protocoltb,SMD,2,restrIndex {} protocoltb,SMD,1,lock 0 protocoltb,MD,2,restrsel {} protocoltb,MD,6,lock 1 membrane,centeryoffset 0 membrane,rotationMaxtrixList {} analyze,basic,alicombo backbone protocoltb,SMD,1,smd 0 protocoltb,MD,2,saveAsTemplate 0 membrane,xmin -33.41010284423828 membrane,ysize 100 protocoltb,SMD,3,smd 0 membrane,axis x protocoltb,SMD,1,saveAsTemplate 0 membrane,xmax 66.58989715576172 protocoltb,MD,3,lock 1 protocoltb,MD,6,restrIndex {} saltconc,0 0.15 protocoltb,MD,3,restrsel {} protocoltb,MD,1,saveAsTemplate 0 protocoltb,MD,1,restrIndex {} protocoltb,MD,0,lock 0 protocoltb,SMD,0,saveAsTemplate 0 protocoltb,SMD,0,restrIndex {} analyze,advance,hbondsel1entry {Type Selection} saltions,0 NaCl protocoltb,MD,1,smd 0 analyze,basic,alicheck 0 membrane,centerxoffset 0 protocoltb,SMD,3,lock 0 protocoltb,MD,3,smd 0 protocoltb,MD,0,saveAsTemplate 0 protocoltb,MD,4,restrsel {} protocoltb,MD,5,smd 0 membrane,rotate,x 0 render,rendertype {Capture Display} membrane,trans,x 0 membrane,rotate,y 0 solvent,0 Explicit solvent,minimalbox 0 protocoltb,MD,7,smd 0 membrane,trans,y 0 membrane,rotate,z 0 protocoltb,MD,4,restrIndex {} membrane,trans,z 0 protocoltb,SMD,0,lock 0 protocoltb,MD,5,lock 1 protocoltb,SMD,3,restrIndex {} protocoltb,SMD,0,restrsel {} protocoltb,MD,5,restrsel {} membrane,ymin -9.142005920410156 protocoltb,MD,2,lock 0 membrane,ymax 90.85799407958984 protocoltb,MD,7,saveAsTemplate 0 protocoltb,MD,7,restrIndex {} protocoltb,SMD,0,smd 0 analyze,basic,selentry {Type Selection} protocoltb,SMD,1,restrsel {} membrane,xsize 100 protocoltb,SMD,2,smd 0 mdff,mdff 50000 protocoltb,MD,6,restrsel {} protocoltb,MD,2,restrIndex {} } array set QWIKMD::chains {2,2 {400 - 444} 0,0 1 1,0 1 0,1 {A and protein} 2,0 1 1,1 {A and hetero} 0,2 {5 - 232} 2,1 {A and water} 1,2 {500 - 508}} array set QWIKMD::index_cmb {{A and water,1} VDW {A and water,2} Name {A and water,3} 2 {A and water,4} rep23 {A and water,5} {chain "A" and water and not (resid "414" and chain "A" and water) and not (resid "424" and chain "A" and water) and not (resid "425" and chain "A" and water) and not (resid "427" and chain "A" and water) and not (resid "431" and chain "A" and water) and not (resid "432" and chain "A" and water) and not (resid "433" and chain "A" and water) and not (resid "437" and chain "A" and water) and not (resid "438" and chain "A" and water) and not (resid "439" and chain "A" and water) and not (resid "441" and chain "A" and water) and not (resid "442" and chain "A" and water) and not (resid "443" and chain "A" and water) and not (resid "444" and chain "A" and water) and not (resid "412" and chain "A" and water) and not (resid "410" and chain "A" and water) and not (resid "405" and chain "A" and water)} {A and hetero,1} Licorice {A and hetero,2} Name {A and hetero,3} 1 {A and protein,1} NewCartoon {A and hetero,4} rep22 {A and protein,2} {0 blue} {A and hetero,5} {chain "A" and qwikmd_hetero and not (resid "500" and chain "A" and qwikmd_hetero) and not (resid "501" and chain "A" and qwikmd_hetero) and not (resid "502" and chain "A" and qwikmd_hetero) and not (resid "503" and chain "A" and qwikmd_hetero) and not (resid "504" and chain "A" and qwikmd_hetero) and not (resid "505" and chain "A" and qwikmd_hetero) and not (resid "506" and chain "A" and qwikmd_hetero) and not (resid "507" and chain "A" and qwikmd_hetero) and not (resid "508" and chain "A" and qwikmd_hetero)} {A and protein,3} 0 {A and protein,4} rep21 {A and protein,5} {chain "A" and qwikmd_protein} } set QWIKMD::delete {500_A 501_A 502_A 503_A 504_A 505_A 506_A 507_A 508_A 414_A 424_A 425_A 427_A 431_A 432_A 433_A 437_A 438_A 439_A 441_A 442_A 443_A 444_A 412_A 410_A 405_A} array set QWIKMD::mutate {} array set QWIKMD::protonate { } set QWIKMD::mutindex {} set QWIKMD::protindex {} set QWIKMD::renameindex {216_A 300_A 216_A} array set QWIKMD::dorename {216_A LYR 300_A LYR} set QWIKMD::patchestr {} set QWIKMD::state 0 set QWIKMD::load 1 set QWIKMD::prevconfFile {Minimization Annealing Equilibration MD MD.1 MD.2 MD.3 MD.4} set QWIKMD::confFile $QWIKMD::prevconfFile set prtclLines {{Minimization 2000 backbone NpT 0 1} {Annealing 144000 backbone NpT 27 1} {Equilibration 500000 backbone NpT 27 1} {MD 5000000 none NpT 27 1} {MD.1 5000000 none NpT 27 1} {MD.2 5000000 none NpT 27 1} {MD.3 5000000 none NpT 27 1} {MD.4 5000000 none NpT 27 1}} for {set i 0} {$i < [llength $prtclLines]} {incr i} { $QWIKMD::advGui(protocoltb,$QWIKMD::run) insert end [lindex $prtclLines $i] if {[file exists [lindex [lindex $prtclLines $i] 0].dcd] == 1} { incr QWIKMD::state } } pbc box -center bb -color yellow -width 4 set QWIKMD::pbcInfo [pbc get -first 0 -last 0] set QWIKMD::basicGui(live) 0 set QWIKMD::dcdfreq 100000 set QWIKMD::smdfreq 40 set QWIKMD::maxSteps {2000 144000 500000 5000000 5000000 5000000 5000000 5000000}