Wed Dec 21 14:20:50 PST 2011 #!/bin/csh -f # input: # $1 receptor coordinates file; # $2 grid size; # $3 # of iterations for the first run; # $4 # of iterations for the second run; # $5 # of iterations for the third run; # output: # delphi map: $1.phi # log file: delphi.out set RECCRG = rec+sph2.crg set GRID = 179 set n1 = 50 set n2 = 120 set n3 = 180 set DELPHI = $DOCK_BASE/private/delphi set VDW = vdw.siz #set VDW = vdw.hydren set CRG = amb2.crg.oxt set PRM = genric.prm # three step focussing calc. if (-e ARCDAT) /bin/rm ARCDAT cp $VDW fort.11 cp $CRG fort.12 cp $RECCRG fort.13 echo "gsize=$GRID, perfil=20, bndcon=2, linit=$n1\n" >! fort.10 cat $PRM >> fort.10 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=60, bndcon=3, linit=$n2\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=90, bndcon=3, linit=$n3\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) /bin/rm fort.1[0-3] fort.18 ARCDAT mv fort.14 $RECCRG:r.phi ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Wed Dec 21 2011 at 14:20:50 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 257 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1960 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6033592 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : dipolar x,y,z periodic bc. flags : F F F # of linear iterations : 50 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 20.00000 xmin,xmax (A): -10.35400 34.96700 ymin,ymax (A): 0.4080001 41.05800 zmin,zma (A): -30.77100 28.23200 x,y,z range (A): 45.32100 40.65000 59.00300 scale (grids/A): 0.6033592 object centre (A): 12.30650 20.73300 -1.269500 number of atom coordinates read : 1960 total number of charged atoms : 1828 net assigned charge : 3.000002 assigned positive charge : 287.9791 centred at (gu) : 89.55192 89.54246 90.58608 assigned negative charge : -284.9793 centred at (gu) : 89.64504 89.67813 90.60783 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 4729 nv = 96 ne = 84 npr = 40836 no. pairs analyzed = 40836 no. exposed pairs = 2488 no. arc points = 17265 no. surface atoms = 848 nbur = 1112 mkacc time = 7.0000008E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 208 mr = 2538 m= 1 mr = 18 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1600000 number of dielectric boundary points 2382 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1746 ## 198 charges are in solution ## iepsmp to db, and charging done at 0.3300000 number of grid points assigned charge 5818 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.8021210E-09 8.5705687E-10 midg,1,midg; midg,igrid,midg 5.9663803E-09 -2.4137483E-09 1,midg,midg; igrid,midg,midg 4.5876942E-09 -1.2479372E-09 gauss-seidel spectral radius is 0.9857254 estimated iterations to convergence 69 setup time was (sec) 0.5700000 now iterating at: 14:20:51 rms-change max change #iterations 9.4872802E-02 15.47254 at 10iterations 7.9544308E-03 1.463713 at 20iterations 6.8132428E-04 0.1253786 at 30iterations 5.7246751E-05 9.2315674E-03 at 40iterations 4.9105543E-06 9.1552734E-04 at 50iterations finished qdiffx linear iterations at : 14:20:56 total time elapsed so far: 5.000000 # loops : 50 mean,max change (kT/e) : 4.9105543E-06 9.1552734E-04 energy calculations done at 5.000000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.140000 DelPhi exited at 14:20:57 5.140u 0.485s 0:06.14 91.5% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Wed Dec 21 2011 at 14:20:57 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 257 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1960 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.810078 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 120 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 60.00000 xmin,xmax (A): -10.35400 34.96700 ymin,ymax (A): 0.4080001 41.05800 zmin,zma (A): -30.77100 28.23200 x,y,z range (A): 45.32100 40.65000 59.00300 scale (grids/A): 1.810078 object centre (A): 12.30650 20.73300 -1.269500 number of atom coordinates read : 1960 total number of charged atoms : 1828 net assigned charge : 3.000002 assigned positive charge : 287.9791 centred at (gu) : 88.65554 88.62749 91.75825 assigned negative charge : -284.9793 centred at (gu) : 88.93521 89.03452 91.82380 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 51362 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17265 grid for indexing accessible points = 1.400000 m= 17182 mr = 35077 m= 2181 mr = 12533 m= 88 mr = 1277 m= 2 mr = 26 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2700000 number of dielectric boundary points 21902 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 153 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 14273 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 0.6033592 object centre at (A) : 12.30650 20.73300 -1.269500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.5275080E-02 2.1150239E-02 midg,1,midg; midg,igrid,midg 4.1778591E-03 -4.9635470E-03 1,midg,midg; igrid,midg,midg -2.3846342E-03 -4.2760465E-03 gauss-seidel spectral radius is 0.9984112 estimated iterations to convergence 199 setup time was (sec) 0.5200000 now iterating at: 14:20:58 rms-change max change #iterations 3.164307 188.7469 at 10iterations 1.400664 58.84159 at 20iterations 0.6184013 25.45896 at 30iterations 0.2712626 10.68678 at 40iterations 0.1197342 4.581194 at 50iterations 5.2640516E-02 2.149834 at 60iterations 2.3194538E-02 0.9005671 at 70iterations 1.0254066E-02 0.3921661 at 80iterations 4.5166700E-03 0.1730356 at 90iterations 1.9877709E-03 7.4563980E-02 at 100iterations 8.7956118E-04 3.3077240E-02 at 110iterations 3.8810720E-04 1.6381264E-02 at 120iterations finished qdiffx linear iterations at : 14:21:06 total time elapsed so far: 8.460000 # loops : 120 mean,max change (kT/e) : 3.8810720E-04 1.6381264E-02 energy calculations done at 8.460000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.600000 DelPhi exited at 14:21:07 8.601u 0.317s 0:10.08 88.3% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Wed Dec 21 2011 at 14:21:07 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 257 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1960 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.715116 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 180 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 90.00000 xmin,xmax (A): -10.35400 34.96700 ymin,ymax (A): 0.4080001 41.05800 zmin,zma (A): -30.77100 28.23200 x,y,z range (A): 45.32100 40.65000 59.00300 scale (grids/A): 2.715116 object centre (A): 12.30650 20.73300 -1.269500 number of atom coordinates read : 1960 total number of charged atoms : 1828 net assigned charge : 3.000002 assigned positive charge : 287.9791 centred at (gu) : 87.98328 87.94129 92.63727 assigned negative charge : -284.9793 centred at (gu) : 88.40285 88.55183 92.73573 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 118788 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17265 grid for indexing accessible points = 1.400000 m= 57223 mr = 84784 m= 18738 mr = 46679 m= 3784 mr = 15135 m= 383 mr = 2657 m= 13 mr = 241 m= 0 mr = 6 time to grow re-entrant surface = 0.4200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8400000 number of dielectric boundary points 49427 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.050000 number of grid points assigned charge 14624 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 1.810078 object centre at (A) : 12.30650 20.73300 -1.269500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1884647 0.1370660 midg,1,midg; midg,igrid,midg 1.0700975E-02 -6.7382380E-02 1,midg,midg; igrid,midg,midg -6.3960634E-02 -7.1536265E-02 gauss-seidel spectral radius is 0.9991773 estimated iterations to convergence 275 setup time was (sec) 1.350000 now iterating at: 14:21:09 rms-change max change #iterations 7.681166 265.9333 at 10iterations 4.323893 130.8695 at 20iterations 2.421757 61.93337 at 30iterations 1.351520 32.96807 at 40iterations 0.7539288 16.21770 at 50iterations 0.4179920 9.139641 at 60iterations 0.2322921 4.986316 at 70iterations 0.1290666 2.835979 at 80iterations 7.1671978E-02 1.515847 at 90iterations 3.9961305E-02 0.9011917 at 100iterations 2.2197379E-02 0.4911423 at 110iterations 1.2356651E-02 0.3071246 at 120iterations 6.8695717E-03 0.1628227 at 130iterations 3.8133801E-03 8.2462788E-02 at 140iterations 2.1178990E-03 4.9264908E-02 at 150iterations 1.1788774E-03 2.6272416E-02 at 160iterations 6.5618707E-04 1.4409065E-02 at 170iterations 3.6399675E-04 7.5759888E-03 at 180iterations finished qdiffx linear iterations at : 14:21:23 total time elapsed so far: 15.76000 # loops : 180 mean,max change (kT/e) : 3.6399675E-04 7.5759888E-03 energy calculations done at 15.76000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.89000 DelPhi exited at 14:21:32 15.893u 0.510s 0:24.87 65.9% 0+0k 0+0io 0pf+0w