Sat Oct 8 22:38:21 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+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 Sat Oct 8 2011 at 22:38:21 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: 247 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3211 !!! WARNING: TPO 1 has a net charge of -1.2740 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.5958757 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): -15.81100 41.91300 ymin,ymax (A): 16.64500 76.38900 zmin,zma (A): 25.33000 82.99500 x,y,z range (A): 57.72400 59.74400 57.66499 scale (grids/A): 0.5958757 object centre (A): 13.05100 46.51700 54.16250 number of atom coordinates read : 3211 total number of charged atoms : 3070 net assigned charge : 12.22603 assigned positive charge : 470.9338 centred at (gu) : 89.30441 90.06332 91.71287 assigned negative charge : -458.7094 centred at (gu) : 89.13811 90.13480 91.94228 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7736 nv = 96 ne = 84 npr = 62999 no. pairs analyzed = 62999 no. exposed pairs = 4288 no. arc points = 30539 no. surface atoms = 1427 nbur = 1784 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 385 mr = 3985 m= 1 mr = 32 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 10 time to turn everything in is 0.3400000 number of dielectric boundary points 4105 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3094 ## 309 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 9722 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.9779322E-09 -6.2773591E-09 midg,1,midg; midg,igrid,midg 7.3626532E-09 2.1021225E-09 1,midg,midg; igrid,midg,midg -1.9317921E-09 9.3514814E-09 gauss-seidel spectral radius is 0.9854900 estimated iterations to convergence 68 setup time was (sec) 0.6000000 now iterating at: 22:38:22 rms-change max change #iterations 0.1167259 15.66652 at 10iterations 9.7106993E-03 1.366879 at 20iterations 8.2602532E-04 0.1082897 at 30iterations 7.7499208E-05 1.2683868E-02 at 40iterations 9.0543808E-06 1.2121201E-03 at 50iterations finished qdiffx linear iterations at : 22:38:25 total time elapsed so far: 3.430000 # loops : 50 mean,max change (kT/e) : 9.0543808E-06 1.2121201E-03 energy calculations done at 3.430000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.610000 DelPhi exited at 22:38:25 3.609u 0.231s 0:04.17 91.8% 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 22:38:25 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: 247 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3211 !!! WARNING: TPO 1 has a net charge of -1.2740 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: 1.787627 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): -15.81100 41.91300 ymin,ymax (A): 16.64500 76.38900 zmin,zma (A): 25.33000 82.99500 x,y,z range (A): 57.72400 59.74400 57.66499 scale (grids/A): 1.787627 object centre (A): 13.05100 46.51700 54.16250 number of atom coordinates read : 3211 total number of charged atoms : 3070 net assigned charge : 12.22603 assigned positive charge : 470.9338 centred at (gu) : 87.91257 90.18961 95.13766 assigned negative charge : -458.7094 centred at (gu) : 87.41420 90.40468 95.82648 start vw surface at 0.1500000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 83849 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30539 grid for indexing accessible points = 1.400000 m= 29071 mr = 55977 m= 4194 mr = 20644 m= 177 mr = 2383 m= 3 mr = 39 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 1791 time to turn everything in is 0.5900000 number of dielectric boundary points 38251 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 239 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7100000 number of grid points assigned charge 23946 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) : 0.5958757 object centre at (A) : 13.05100 46.51700 54.16250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.7856249E-02 5.3352816E-03 midg,1,midg; midg,igrid,midg 5.0197572E-02 2.1317946E-02 1,midg,midg; igrid,midg,midg -6.6396510E-03 3.5868745E-02 gauss-seidel spectral radius is 0.9985296 estimated iterations to convergence 207 setup time was (sec) 0.9100000 now iterating at: 22:38:26 rms-change max change #iterations 4.111522 172.9771 at 10iterations 1.852777 60.65630 at 20iterations 0.8440568 26.59098 at 30iterations 0.3837650 11.58372 at 40iterations 0.1738580 5.490671 at 50iterations 7.8746863E-02 2.426147 at 60iterations 3.5879552E-02 1.157587 at 70iterations 1.6310440E-02 0.4898071 at 80iterations 7.4249627E-03 0.2391663 at 90iterations 3.3918074E-03 0.1073408 at 100iterations 1.5384819E-03 4.9682483E-02 at 110iterations 6.9635740E-04 2.2110939E-02 at 120iterations finished qdiffx linear iterations at : 22:38:33 total time elapsed so far: 7.990000 # loops : 120 mean,max change (kT/e) : 6.9635740E-04 2.2110939E-02 energy calculations done at 7.990000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.150000 DelPhi exited at 22:38:34 8.157u 0.288s 0:08.76 96.2% 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 Sat Oct 8 2011 at 22:38:34 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: 247 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3211 !!! WARNING: TPO 1 has a net charge of -1.2740 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: 2.681441 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): -15.81100 41.91300 ymin,ymax (A): 16.64500 76.38900 zmin,zma (A): 25.33000 82.99500 x,y,z range (A): 57.72400 59.74400 57.66499 scale (grids/A): 2.681441 object centre (A): 13.05100 46.51700 54.16250 number of atom coordinates read : 3211 total number of charged atoms : 3070 net assigned charge : 12.22603 assigned positive charge : 470.9338 centred at (gu) : 86.86848 90.28409 97.70610 assigned negative charge : -458.7094 centred at (gu) : 86.12129 90.60693 98.73988 start vw surface at 0.1600000 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 194154 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30539 grid for indexing accessible points = 1.400000 m= 94387 mr = 136693 m= 32761 mr = 75202 m= 7067 mr = 25509 m= 769 mr = 4959 m= 28 mr = 446 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.8500000 no. cavity mid-points inaccessible to solvent = 6186 time to turn everything in is 1.480000 number of dielectric boundary points 86358 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.630000 number of grid points assigned charge 24535 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) : 1.787627 object centre at (A) : 13.05100 46.51700 54.16250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.6641073 0.1440062 midg,1,midg; midg,igrid,midg 0.6574160 0.5331019 1,midg,midg; igrid,midg,midg 7.8896433E-03 0.5814872 gauss-seidel spectral radius is 0.9992592 estimated iterations to convergence 290 setup time was (sec) 1.820000 now iterating at: 22:38:36 rms-change max change #iterations 10.18832 373.9691 at 10iterations 6.014200 156.3992 at 20iterations 3.525386 82.48500 at 30iterations 2.057837 42.55785 at 40iterations 1.196791 22.35039 at 50iterations 0.6921479 14.07518 at 60iterations 0.4006028 8.262900 at 70iterations 0.2310740 4.314823 at 80iterations 0.1333588 2.317240 at 90iterations 7.6828033E-02 1.497571 at 100iterations 4.4136204E-02 0.8321953 at 110iterations 2.5403703E-02 0.4427342 at 120iterations 1.4596868E-02 0.2830743 at 130iterations 8.3960239E-03 0.1505995 at 140iterations 4.8271106E-03 0.1053238 at 150iterations 2.7745997E-03 4.9034119E-02 at 160iterations 1.5908100E-03 2.8846741E-02 at 170iterations 9.1257098E-04 1.5754700E-02 at 180iterations finished qdiffx linear iterations at : 22:38:48 total time elapsed so far: 13.52000 # loops : 180 mean,max change (kT/e) : 9.1257098E-04 1.5754700E-02 energy calculations done at 13.52000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.70000 DelPhi exited at 22:38:48 13.699u 0.280s 0:14.25 98.0% 0+0k 0+0io 0pf+0w