Sat Oct 8 20:05:21 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 Sat Oct 8 2011 at 20:05:21 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: 266 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2619 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN7 741 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6186570 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): -32.09500 17.56300 ymin,ymax (A): -23.61600 22.98000 zmin,zma (A): -12.45000 45.09400 x,y,z range (A): 49.65800 46.59600 57.54400 scale (grids/A): 0.6186570 object centre (A): -7.266001 -0.3179998 16.32200 number of atom coordinates read : 2619 total number of charged atoms : 2475 net assigned charge : 3.500007 assigned positive charge : 397.0500 centred at (gu) : 88.74663 89.22705 89.62009 assigned negative charge : -393.5505 centred at (gu) : 88.65366 89.28610 89.51194 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 6474 nv = 96 ne = 84 npr = 55095 no. pairs analyzed = 55095 no. exposed pairs = 3017 no. arc points = 21738 no. surface atoms = 1015 nbur = 1604 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 315 mr = 3579 m= 2 mr = 42 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 119 time to turn everything in is 0.3100000 number of dielectric boundary points 3170 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2247 ## 245 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 8178 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.6891433E-09 8.9157508E-09 midg,1,midg; midg,igrid,midg 7.8085396E-09 -8.6758012E-10 1,midg,midg; igrid,midg,midg -4.4234323E-09 6.6353549E-09 gauss-seidel spectral radius is 0.9864661 estimated iterations to convergence 70 setup time was (sec) 0.6100000 now iterating at: 20:05:22 rms-change max change #iterations 0.1248285 19.98762 at 10iterations 1.1455048E-02 1.665943 at 20iterations 1.0360391E-03 0.1455498 at 30iterations 9.5902695E-05 1.3607025E-02 at 40iterations 8.7680064E-06 1.3132095E-03 at 50iterations finished qdiffx linear iterations at : 20:05:26 total time elapsed so far: 4.320000 # loops : 50 mean,max change (kT/e) : 8.7680064E-06 1.3132095E-03 energy calculations done at 4.320000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.480000 DelPhi exited at 20:05:26 4.485u 0.418s 0:05.17 94.5% 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 Sat Oct 8 2011 at 20:05:26 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: 266 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2619 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN7 741 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.855971 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): -32.09500 17.56300 ymin,ymax (A): -23.61600 22.98000 zmin,zma (A): -12.45000 45.09400 x,y,z range (A): 49.65800 46.59600 57.54400 scale (grids/A): 1.855971 object centre (A): -7.266001 -0.3179998 16.32200 number of atom coordinates read : 2619 total number of charged atoms : 2475 net assigned charge : 3.500007 assigned positive charge : 397.0500 centred at (gu) : 86.23940 87.68079 88.85985 assigned negative charge : -393.5505 centred at (gu) : 85.96068 87.85802 88.53576 start vw surface at 0.1200000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 71022 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21738 grid for indexing accessible points = 1.400000 m= 23726 mr = 49616 m= 3189 mr = 17370 m= 147 mr = 1945 m= 2 mr = 46 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 6177 time to turn everything in is 0.5600000 number of dielectric boundary points 29109 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 172 iepsmp to db, and charging done at 0.6600000 number of grid points assigned charge 19407 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) : 0.6186570 object centre at (A) : -7.266001 -0.3179998 16.32200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.8994836E-03 2.7369443E-02 midg,1,midg; midg,igrid,midg 1.3244745E-02 3.1292249E-04 1,midg,midg; igrid,midg,midg -5.7906788E-03 3.0937681E-02 gauss-seidel spectral radius is 0.9985635 estimated iterations to convergence 209 setup time was (sec) 0.8400000 now iterating at: 20:05:28 rms-change max change #iterations 4.029430 165.1043 at 10iterations 1.854566 59.59756 at 20iterations 0.8506220 30.58719 at 30iterations 0.3907950 12.71949 at 40iterations 0.1798699 5.787704 at 50iterations 8.2525656E-02 2.793730 at 60iterations 3.8013648E-02 1.180481 at 70iterations 1.7406266E-02 0.5697155 at 80iterations 8.0151754E-03 0.2617922 at 90iterations 3.6781980E-03 0.1108255 at 100iterations 1.6891080E-03 5.4357529E-02 at 110iterations 7.7812659E-04 2.7687073E-02 at 120iterations finished qdiffx linear iterations at : 20:05:37 total time elapsed so far: 10.20000 # loops : 120 mean,max change (kT/e) : 7.7812659E-04 2.7687073E-02 energy calculations done at 10.20000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.37000 DelPhi exited at 20:05:38 10.372u 0.464s 0:11.09 97.6% 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 Sat Oct 8 2011 at 20:05:38 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: 266 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2619 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN7 741 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.783957 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): -32.09500 17.56300 ymin,ymax (A): -23.61600 22.98000 zmin,zma (A): -12.45000 45.09400 x,y,z range (A): 49.65800 46.59600 57.54400 scale (grids/A): 2.783957 object centre (A): -7.266001 -0.3179998 16.32200 number of atom coordinates read : 2619 total number of charged atoms : 2475 net assigned charge : 3.500007 assigned positive charge : 397.0500 centred at (gu) : 84.35885 86.52122 88.28976 assigned negative charge : -393.5505 centred at (gu) : 83.94100 86.78690 87.80354 start vw surface at 0.1200000 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 164543 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21738 grid for indexing accessible points = 1.400000 m= 79427 mr = 120252 m= 25752 mr = 64977 m= 5528 mr = 20479 m= 703 mr = 4098 m= 43 mr = 480 m= 1 mr = 16 m= 0 mr = 0 time to grow re-entrant surface = 0.8500000 no. cavity mid-points inaccessible to solvent = 20671 time to turn everything in is 1.450000 number of dielectric boundary points 65695 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.580000 number of grid points assigned charge 19799 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) : 1.855971 object centre at (A) : -7.266001 -0.3179998 16.32200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.1579325E-02 0.3767550 midg,1,midg; midg,igrid,midg 0.1579149 2.8427946E-03 1,midg,midg; igrid,midg,midg -4.9733136E-02 0.4094084 gauss-seidel spectral radius is 0.9992324 estimated iterations to convergence 285 setup time was (sec) 1.780000 now iterating at: 20:05:40 rms-change max change #iterations 9.480533 312.7739 at 10iterations 5.428804 130.6109 at 20iterations 3.093950 66.09372 at 30iterations 1.759111 44.27631 at 40iterations 1.002194 21.84549 at 50iterations 0.5699453 13.12284 at 60iterations 0.3241286 5.932045 at 70iterations 0.1840192 3.887763 at 80iterations 0.1048352 2.320351 at 90iterations 5.9514936E-02 1.201653 at 100iterations 3.3734251E-02 0.6367245 at 110iterations 1.9194050E-02 0.3628950 at 120iterations 1.0901584E-02 0.2025127 at 130iterations 6.1854082E-03 0.1247139 at 140iterations 3.5195271E-03 6.6661835E-02 at 150iterations 1.9995929E-03 3.6148071E-02 at 160iterations 1.1338883E-03 2.0490646E-02 at 170iterations 6.4404495E-04 1.2339592E-02 at 180iterations finished qdiffx linear iterations at : 20:05:56 total time elapsed so far: 17.59000 # loops : 180 mean,max change (kT/e) : 6.4404495E-04 1.2339592E-02 energy calculations done at 17.59000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.75000 DelPhi exited at 20:05:56 17.758u 0.483s 0:18.51 98.4% 0+0k 0+0io 0pf+0w