Tue Nov 22 14:10:36 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 Tue Nov 22 2011 at 14:10:36 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: 251 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1934 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: 0.5746755 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): -41.05100 3.761000 ymin,ymax (A): 13.18400 55.90800 zmin,zma (A): -3.690000 58.25800 x,y,z range (A): 44.81200 42.72400 61.94800 scale (grids/A): 0.5746755 object centre (A): -18.64500 34.54600 27.28400 number of atom coordinates read : 1934 total number of charged atoms : 1802 net assigned charge : 5.000010 assigned positive charge : 289.8060 centred at (gu) : 89.46075 89.64002 90.00002 assigned negative charge : -284.8063 centred at (gu) : 89.52056 89.53603 89.99989 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.0000000E-02 boundary points on vw surface= 4207 nv = 96 ne = 84 npr = 39762 no. pairs analyzed = 39762 no. exposed pairs = 2403 no. arc points = 16910 no. surface atoms = 821 nbur = 1113 mkacc time = 7.0000000E-02 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= 178 mr = 2236 m= 1 mr = 11 m= 0 mr = 0 time to grow re-entrant surface = 8.0000006E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1500000 number of dielectric boundary points 2139 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1699 ## 199 charges are in solution ## iepsmp to db, and charging done at 0.2300000 number of grid points assigned charge 5280 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.0646446E-10 9.0971275E-10 midg,1,midg; midg,igrid,midg -3.7011672E-10 1.9489739E-09 1,midg,midg; igrid,midg,midg 1.8262345E-09 1.7798563E-10 gauss-seidel spectral radius is 0.9842860 estimated iterations to convergence 66 setup time was (sec) 0.3700000 now iterating at: 14:10:37 rms-change max change #iterations 7.6928556E-02 14.20184 at 10iterations 5.9849643E-03 1.148468 at 20iterations 4.4062073E-04 9.7928047E-02 at 30iterations 3.4105236E-05 6.9770813E-03 at 40iterations 2.5760530E-06 4.8446655E-04 at 50iterations finished qdiffx linear iterations at : 14:10:43 total time elapsed so far: 3.470000 # loops : 50 mean,max change (kT/e) : 2.5760530E-06 4.8446655E-04 energy calculations done at 3.470000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.610000 DelPhi exited at 14:10:44 3.617u 0.211s 0:07.75 49.2% 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 Tue Nov 22 2011 at 14:10:44 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: 251 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1934 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: 1.724027 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): -41.05100 3.761000 ymin,ymax (A): 13.18400 55.90800 zmin,zma (A): -3.690000 58.25800 x,y,z range (A): 44.81200 42.72400 61.94800 scale (grids/A): 1.724027 object centre (A): -18.64500 34.54600 27.28400 number of atom coordinates read : 1934 total number of charged atoms : 1802 net assigned charge : 5.000010 assigned positive charge : 289.8060 centred at (gu) : 88.38209 88.91992 90.00001 assigned negative charge : -284.8063 centred at (gu) : 88.56190 88.60825 89.99995 start vw surface at 5.9999999E-02 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 45820 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16910 grid for indexing accessible points = 1.400000 m= 14888 mr = 31070 m= 1764 mr = 10919 m= 59 mr = 965 m= 0 mr = 3 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 1526 time to turn everything in is 0.2400000 number of dielectric boundary points 19574 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 179 iepsmp to db, and charging done at 0.3300000 number of grid points assigned charge 13979 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) : 0.5746755 object centre at (A) : -18.64500 34.54600 27.28400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.0939995E-02 1.8511273E-02 midg,1,midg; midg,igrid,midg -2.0068975E-03 3.7636927E-03 1,midg,midg; igrid,midg,midg 6.6637690E-04 2.0611142E-03 gauss-seidel spectral radius is 0.9982511 estimated iterations to convergence 190 setup time was (sec) 0.4800000 now iterating at: 14:10:44 rms-change max change #iterations 2.932057 154.9959 at 10iterations 1.244728 51.48919 at 20iterations 0.5260592 22.80854 at 30iterations 0.2224731 9.334525 at 40iterations 9.4558120E-02 3.922712 at 50iterations 4.0102385E-02 1.690429 at 60iterations 1.6937455E-02 0.6502042 at 70iterations 7.1589728E-03 0.2871437 at 80iterations 3.0429675E-03 0.1204891 at 90iterations 1.2900565E-03 5.1636726E-02 at 100iterations 5.4632640E-04 2.3109436E-02 at 110iterations 2.3091251E-04 9.2382431E-03 at 120iterations finished qdiffx linear iterations at : 14:11:01 total time elapsed so far: 8.210000 # loops : 120 mean,max change (kT/e) : 2.3091251E-04 9.2382431E-03 energy calculations done at 8.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.340000 DelPhi exited at 14:11:02 8.342u 0.240s 0:18.08 47.4% 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 Tue Nov 22 2011 at 14:11:02 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: 251 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1934 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: 2.586040 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): -41.05100 3.761000 ymin,ymax (A): 13.18400 55.90800 zmin,zma (A): -3.690000 58.25800 x,y,z range (A): 44.81200 42.72400 61.94800 scale (grids/A): 2.586040 object centre (A): -18.64500 34.54600 27.28400 number of atom coordinates read : 1934 total number of charged atoms : 1802 net assigned charge : 5.000010 assigned positive charge : 289.8060 centred at (gu) : 87.57332 88.37991 90.00005 assigned negative charge : -284.8063 centred at (gu) : 87.84291 87.91246 89.99993 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 106029 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16910 grid for indexing accessible points = 1.400000 m= 50224 mr = 75256 m= 15730 mr = 40997 m= 2924 mr = 12571 m= 250 mr = 2064 m= 4 mr = 104 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 5318 time to turn everything in is 0.6000000 number of dielectric boundary points 44169 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 8 iepsmp to db, and charging done at 0.6900000 number of grid points assigned charge 14415 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) : 1.724027 object centre at (A) : -18.64500 34.54600 27.28400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1929047 0.1646218 midg,1,midg; midg,igrid,midg -4.5618974E-02 2.3330566E-02 1,midg,midg; igrid,midg,midg -2.1388533E-02 1.7311189E-02 gauss-seidel spectral radius is 0.9991243 estimated iterations to convergence 267 setup time was (sec) 0.8600000 now iterating at: 14:11:03 rms-change max change #iterations 7.247351 274.0057 at 10iterations 3.994782 126.2886 at 20iterations 2.191676 54.56087 at 30iterations 1.194915 30.03353 at 40iterations 0.6540121 16.02977 at 50iterations 0.3558196 7.901566 at 60iterations 0.1944094 4.533331 at 70iterations 0.1059114 2.389732 at 80iterations 5.7753164E-02 1.403313 at 90iterations 3.1409301E-02 0.7081592 at 100iterations 1.7147237E-02 0.4017372 at 110iterations 9.3552852E-03 0.2286949 at 120iterations 5.0876038E-03 0.1200790 at 130iterations 2.7755464E-03 6.1471939E-02 at 140iterations 1.5155538E-03 3.6975861E-02 at 150iterations 8.2571030E-04 2.0477295E-02 at 160iterations 4.5105166E-04 9.7198486E-03 at 170iterations 2.4568723E-04 5.7273507E-03 at 180iterations finished qdiffx linear iterations at : 14:11:27 total time elapsed so far: 12.70000 # loops : 180 mean,max change (kT/e) : 2.4568723E-04 5.7273507E-03 energy calculations done at 12.70000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.84000 DelPhi exited at 14:11:28 12.842u 0.232s 0:26.63 49.0% 0+0k 0+0io 0pf+0w