Mon Oct 10 23:39:13 PDT 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+sph.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 = amb.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 Mon Oct 10 2011 at 23:39:14 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2623 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5679914 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): 10.97000 64.60900 ymin,ymax (A): -3.629000 59.04800 zmin,zma (A): 10.87700 54.09300 x,y,z range (A): 53.63900 62.67700 43.21600 scale (grids/A): 0.5679914 object centre (A): 37.78950 27.70950 32.48500 number of atom coordinates read : 2623 total number of charged atoms : 2483 net assigned charge : 9.000021 assigned positive charge : 394.9107 centred at (gu) : 88.92882 91.41844 89.78611 assigned negative charge : -385.9114 centred at (gu) : 88.93650 91.28038 89.90533 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 5485 nv = 96 ne = 84 npr = 52598 no. pairs analyzed = 52598 no. exposed pairs = 3176 no. arc points = 22253 no. surface atoms = 1072 nbur = 1551 mkacc time = 0.1600000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 251 mr = 2986 m= 1 mr = 16 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 8 time to turn everything in is 0.3800000 number of dielectric boundary points 2735 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2244 ## 254 charges are in solution ## iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 7036 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.8836715E-09 -2.6867139E-10 midg,1,midg; midg,igrid,midg -3.6334483E-10 4.1774424E-09 1,midg,midg; igrid,midg,midg 1.7288300E-09 9.0153052E-10 gauss-seidel spectral radius is 0.9839743 estimated iterations to convergence 65 setup time was (sec) 0.6600000 now iterating at: 23:39:14 rms-change max change #iterations 8.3348833E-02 15.39156 at 10iterations 7.0660664E-03 1.104382 at 20iterations 9.2704879E-04 0.2292023 at 30iterations 2.0948934E-04 5.6198120E-02 at 40iterations 5.2011230E-05 1.3999939E-02 at 50iterations finished qdiffx linear iterations at : 23:39:18 total time elapsed so far: 3.810000 # loops : 50 mean,max change (kT/e) : 5.2011230E-05 1.3999939E-02 energy calculations done at 3.810000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.050000 DelPhi exited at 23:39:18 4.049u 0.167s 0:04.58 91.7% 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 Mon Oct 10 2011 at 23:39:18 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2623 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.703974 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): 10.97000 64.60900 ymin,ymax (A): -3.629000 59.04800 zmin,zma (A): 10.87700 54.09300 x,y,z range (A): 53.63900 62.67700 43.21600 scale (grids/A): 1.703974 object centre (A): 37.78950 27.70950 32.48500 number of atom coordinates read : 2623 total number of charged atoms : 2483 net assigned charge : 9.000021 assigned positive charge : 394.9107 centred at (gu) : 86.78595 94.25446 89.35745 assigned negative charge : -385.9114 centred at (gu) : 86.80941 93.84090 89.71584 start vw surface at 0.2000000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 60431 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22253 grid for indexing accessible points = 1.400000 m= 19752 mr = 41793 m= 2290 mr = 14061 m= 75 mr = 1205 m= 0 mr = 1 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 466 time to turn everything in is 0.5800000 number of dielectric boundary points 25488 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 264 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.7200000 number of grid points assigned charge 19236 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) : 0.5679914 object centre at (A) : 37.78950 27.70950 32.48500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.7765330E-02 2.0824843E-03 midg,1,midg; midg,igrid,midg 3.8923710E-04 -7.4951933E-03 1,midg,midg; igrid,midg,midg 3.4522007E-03 9.1286162E-03 gauss-seidel spectral radius is 0.9982956 estimated iterations to convergence 192 setup time was (sec) 0.9100000 now iterating at: 23:39:19 rms-change max change #iterations 3.323382 146.9897 at 10iterations 1.414524 58.62125 at 20iterations 0.6095302 24.18139 at 30iterations 0.2610399 9.887199 at 40iterations 0.1126882 4.173033 at 50iterations 4.8054993E-02 1.654789 at 60iterations 2.0768330E-02 0.7589397 at 70iterations 9.0299537E-03 0.3500977 at 80iterations 4.0171924E-03 0.1577263 at 90iterations 1.8408127E-03 8.3019257E-02 at 100iterations 8.9122658E-04 3.8887024E-02 at 110iterations 4.5659297E-04 2.1644592E-02 at 120iterations finished qdiffx linear iterations at : 23:39:27 total time elapsed so far: 8.680000 # loops : 120 mean,max change (kT/e) : 4.5659297E-04 2.1644592E-02 energy calculations done at 8.680000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.920000 DelPhi exited at 23:39:28 8.923u 0.229s 0:09.57 95.5% 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 Mon Oct 10 2011 at 23:39:28 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2623 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.555961 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): 10.97000 64.60900 ymin,ymax (A): -3.629000 59.04800 zmin,zma (A): 10.87700 54.09300 x,y,z range (A): 53.63900 62.67700 43.21600 scale (grids/A): 2.555961 object centre (A): 37.78950 27.70950 32.48500 number of atom coordinates read : 2623 total number of charged atoms : 2483 net assigned charge : 9.000021 assigned positive charge : 394.9107 centred at (gu) : 85.17867 96.38161 89.03603 assigned negative charge : -385.9114 centred at (gu) : 85.21408 95.76125 89.57365 start vw surface at 0.1900000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 140390 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22253 grid for indexing accessible points = 1.400000 m= 66953 mr = 101914 m= 20720 mr = 54082 m= 3800 mr = 16048 m= 275 mr = 2550 m= 13 mr = 91 m= 0 mr = 3 time to grow re-entrant surface = 0.7700000 no. cavity mid-points inaccessible to solvent = 1760 time to turn everything in is 1.350000 number of dielectric boundary points 57463 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 18 iepsmp to db, and charging done at 1.510000 number of grid points assigned charge 19860 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) : 1.703974 object centre at (A) : 37.78950 27.70950 32.48500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2273818 4.3591753E-02 midg,1,midg; midg,igrid,midg -9.3968935E-02 -0.4638954 1,midg,midg; igrid,midg,midg 6.2772853E-04 9.0016961E-02 gauss-seidel spectral radius is 0.9991564 estimated iterations to convergence 272 setup time was (sec) 1.700000 now iterating at: 23:39:30 rms-change max change #iterations 8.352108 269.0444 at 10iterations 4.659748 108.4300 at 20iterations 2.604631 61.86732 at 30iterations 1.446160 32.05568 at 40iterations 0.8065051 18.02370 at 50iterations 0.4469402 9.290339 at 60iterations 0.2476378 5.190360 at 70iterations 0.1373959 2.912141 at 80iterations 7.6044738E-02 1.752392 at 90iterations 4.2228907E-02 0.9091823 at 100iterations 2.3380255E-02 0.4851665 at 110iterations 1.3040589E-02 0.2731934 at 120iterations 7.2806743E-03 0.1472263 at 130iterations 4.0896637E-03 0.1105881 at 140iterations 2.3348969E-03 5.0338745E-02 at 150iterations 1.3667019E-03 3.3168793E-02 at 160iterations 8.2746858E-04 2.3471832E-02 at 170iterations 5.2308571E-04 1.5316010E-02 at 180iterations finished qdiffx linear iterations at : 23:39:41 total time elapsed so far: 13.38000 # loops : 180 mean,max change (kT/e) : 5.2308571E-04 1.5316010E-02 energy calculations done at 13.38000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.61000 DelPhi exited at 23:39:42 13.612u 0.206s 0:14.24 96.9% 0+0k 0+0io 0pf+0w