Mon Oct 10 16:01:36 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+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 Mon Oct 10 2011 at 16:01:36 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: 306 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5125 !!! WARNING: GLM 134 has a net charge of -0.0940 !!! WARNING: HIR 295 has a net charge of 0.5140 !!! WARNING: HIR 299 has a net charge of 0.5140 !!! WARNING: ASP 610 has a net charge of -2.0000 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: 0.5153594 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): -20.06300 49.01500 ymin,ymax (A): 10.04300 72.89799 zmin,zma (A): 33.71600 95.68200 x,y,z range (A): 69.07800 62.85500 61.96600 scale (grids/A): 0.5153594 object centre (A): 14.47600 41.47050 64.69900 number of atom coordinates read : 5125 total number of charged atoms : 4960 net assigned charge : 1.434018 assigned positive charge : 774.0222 centred at (gu) : 90.13408 90.99091 90.33810 assigned negative charge : -772.5931 centred at (gu) : 90.13154 90.94991 90.33543 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 8441 nv = 96 ne = 84 npr = 106060 no. pairs analyzed = 106060 no. exposed pairs = 6148 no. arc points = 40985 no. surface atoms = 2071 nbur = 3054 mkacc time = 0.1900000 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 = 1.652000 m= 322 mr = 4611 m= 0 mr = 10 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3500000 number of dielectric boundary points 4142 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4061 ## 556 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 11441 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.3137603E-11 3.5557567E-11 midg,1,midg; midg,igrid,midg -9.0657898E-11 2.1249302E-10 1,midg,midg; igrid,midg,midg 1.4233442E-11 3.3276756E-11 gauss-seidel spectral radius is 0.9807569 estimated iterations to convergence 60 setup time was (sec) 0.5400000 now iterating at: 16:01:37 rms-change max change #iterations 7.4918203E-02 12.10516 at 10iterations 5.0722877E-03 0.7786484 at 20iterations 1.0023343E-03 0.1572151 at 30iterations 3.9220907E-04 5.2398682E-02 at 40iterations 1.6917940E-04 2.3197174E-02 at 50iterations finished qdiffx linear iterations at : 16:01:40 total time elapsed so far: 3.440000 # loops : 50 mean,max change (kT/e) : 1.6917940E-04 2.3197174E-02 energy calculations done at 3.440000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.570000 DelPhi exited at 16:01:40 3.577u 0.178s 0:04.09 91.4% 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 Mon Oct 10 2011 at 16:01:40 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: 306 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5125 !!! WARNING: GLM 134 has a net charge of -0.0940 !!! WARNING: HIR 295 has a net charge of 0.5140 !!! WARNING: HIR 299 has a net charge of 0.5140 !!! WARNING: ASP 610 has a net charge of -2.0000 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: 1.546078 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): -20.06300 49.01500 ymin,ymax (A): 10.04300 72.89799 zmin,zma (A): 33.71600 95.68200 x,y,z range (A): 69.07800 62.85500 61.96600 scale (grids/A): 1.546078 object centre (A): 14.47600 41.47050 64.69900 number of atom coordinates read : 5125 total number of charged atoms : 4960 net assigned charge : 1.434018 assigned positive charge : 774.0222 centred at (gu) : 90.40067 92.97107 91.01259 assigned negative charge : -772.5931 centred at (gu) : 90.39406 92.84930 91.00565 start vw surface at 0.1300000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 96291 reading accessible surface arcs data from file ARCDAT no. of arc points read = 40985 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 28430 mr = 68401 m= 2588 mr = 19236 m= 48 mr = 1201 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 630 time to turn everything in is 0.4600000 number of dielectric boundary points 38519 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 520 ## 6 charges are in solution ## iepsmp to db, and charging done at 0.5400000 number of grid points assigned charge 37434 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) : 0.5153594 object centre at (A) : 14.47600 41.47050 64.69900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.7583122E-03 1.3606916E-02 midg,1,midg; midg,igrid,midg -6.8877470E-03 -1.8528593E-04 1,midg,midg; igrid,midg,midg -2.7339756E-02 -3.4939884E-03 gauss-seidel spectral radius is 0.9981710 estimated iterations to convergence 186 setup time was (sec) 0.6800000 now iterating at: 16:01:41 rms-change max change #iterations 4.059494 164.0604 at 10iterations 1.676923 54.23494 at 20iterations 0.7001204 20.68154 at 30iterations 0.2913565 9.092220 at 40iterations 0.1215287 3.879311 at 50iterations 5.0908960E-02 1.545543 at 60iterations 2.1286113E-02 0.6515846 at 70iterations 9.0068998E-03 0.2974854 at 80iterations 3.9769914E-03 0.1168633 at 90iterations 1.8743778E-03 5.8216095E-02 at 100iterations 1.0158614E-03 3.3355713E-02 at 110iterations 6.4193341E-04 1.8310547E-02 at 120iterations finished qdiffx linear iterations at : 16:01:48 total time elapsed so far: 7.830000 # loops : 120 mean,max change (kT/e) : 6.4193341E-04 1.8310547E-02 energy calculations done at 7.830000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.970000 DelPhi exited at 16:01:49 7.972u 0.202s 0:08.73 93.5% 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 16:01:49 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: 306 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5125 !!! WARNING: GLM 134 has a net charge of -0.0940 !!! WARNING: HIR 295 has a net charge of 0.5140 !!! WARNING: HIR 299 has a net charge of 0.5140 !!! WARNING: ASP 610 has a net charge of -2.0000 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: 2.319117 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): -20.06300 49.01500 ymin,ymax (A): 10.04300 72.89799 zmin,zma (A): 33.71600 95.68200 x,y,z range (A): 69.07800 62.85500 61.96600 scale (grids/A): 2.319117 object centre (A): 14.47600 41.47050 64.69900 number of atom coordinates read : 5125 total number of charged atoms : 4960 net assigned charge : 1.434018 assigned positive charge : 774.0222 centred at (gu) : 90.60052 94.45626 91.51829 assigned negative charge : -772.5931 centred at (gu) : 90.59102 94.27394 91.50836 start vw surface at 0.1500000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 224761 reading accessible surface arcs data from file ARCDAT no. of arc points read = 40985 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 101918 mr = 167831 m= 26416 mr = 80235 m= 3823 mr = 19595 m= 201 mr = 2477 m= 1 mr = 58 m= 0 mr = 0 time to grow re-entrant surface = 0.6500000 no. cavity mid-points inaccessible to solvent = 2071 time to turn everything in is 1.160000 number of dielectric boundary points 86924 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 56 iepsmp to db, and charging done at 1.250000 number of grid points assigned charge 39578 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) : 1.546078 object centre at (A) : 14.47600 41.47050 64.69900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.3943208E-02 0.2212795 midg,1,midg; midg,igrid,midg -0.1352893 -2.1247493E-02 1,midg,midg; igrid,midg,midg -0.6243497 9.4900522E-03 gauss-seidel spectral radius is 0.9991788 estimated iterations to convergence 276 setup time was (sec) 1.400000 now iterating at: 16:01:51 rms-change max change #iterations 10.90016 367.0388 at 10iterations 6.291472 161.4580 at 20iterations 3.610283 77.87024 at 30iterations 2.057613 39.76009 at 40iterations 1.171282 25.01590 at 50iterations 0.6634192 13.12001 at 60iterations 0.3745414 6.770194 at 70iterations 0.2113132 3.744997 at 80iterations 0.1187253 2.214848 at 90iterations 6.6944644E-02 1.429754 at 100iterations 3.7525143E-02 0.7499781 at 110iterations 2.1100562E-02 0.4052172 at 120iterations 1.1850614E-02 0.2127533 at 130iterations 6.6752722E-03 0.1138229 at 140iterations 3.7928624E-03 6.6780090E-02 at 150iterations 2.1879936E-03 4.0835857E-02 at 160iterations 1.2943313E-03 2.3132324E-02 at 170iterations 8.0030609E-04 1.4123917E-02 at 180iterations finished qdiffx linear iterations at : 16:02:02 total time elapsed so far: 12.99000 # loops : 180 mean,max change (kT/e) : 8.0030609E-04 1.4123917E-02 energy calculations done at 12.99000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.12000 DelPhi exited at 16:02:03 13.120u 0.208s 0:13.66 97.5% 0+0k 0+0io 0pf+0w