Wed Dec 21 14:21:03 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+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 Wed Dec 21 2011 at 14:21:03 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: 239 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1959 !!! WARNING: ASH 125 has a net charge of -0.3190 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6504421 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): -3.617000 48.51500 ymin,ymax (A): -4.999000 34.78500 zmin,zma (A): -23.52200 31.21000 x,y,z range (A): 52.13200 39.78400 54.73200 scale (grids/A): 0.6504421 object centre (A): 22.44900 14.89300 3.844001 number of atom coordinates read : 1959 total number of charged atoms : 1826 net assigned charge : 4.681008 assigned positive charge : 286.9501 centred at (gu) : 92.41302 89.41730 89.95797 assigned negative charge : -282.2693 centred at (gu) : 92.54399 89.28361 89.88227 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 5669 nv = 96 ne = 84 npr = 40329 no. pairs analyzed = 40329 no. exposed pairs = 2482 no. arc points = 17498 no. surface atoms = 839 nbur = 1120 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 288 mr = 3143 m= 0 mr = 26 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2800000 number of dielectric boundary points 2788 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1793 ## 186 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 6643 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.1226571E-09 1.7823206E-08 midg,1,midg; midg,igrid,midg -6.2992025E-09 2.1500663E-08 1,midg,midg; igrid,midg,midg 1.4548635E-08 -9.2288266E-09 gauss-seidel spectral radius is 0.9876948 estimated iterations to convergence 74 setup time was (sec) 0.5600000 now iterating at: 14:21:04 rms-change max change #iterations 0.1274427 18.18477 at 10iterations 1.2923103E-02 1.976786 at 20iterations 1.3115582E-03 0.1933212 at 30iterations 1.3707644E-04 2.3929596E-02 at 40iterations 1.4058706E-05 2.5825500E-03 at 50iterations finished qdiffx linear iterations at : 14:21:08 total time elapsed so far: 4.660000 # loops : 50 mean,max change (kT/e) : 1.4058706E-05 2.5825500E-03 energy calculations done at 4.660000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.840000 DelPhi exited at 14:21:09 4.843u 0.289s 0:05.55 92.2% 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 Wed Dec 21 2011 at 14:21:09 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: 239 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1959 !!! WARNING: ASH 125 has a net charge of -0.3190 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.951326 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): -3.617000 48.51500 ymin,ymax (A): -4.999000 34.78500 zmin,zma (A): -23.52200 31.21000 x,y,z range (A): 52.13200 39.78400 54.73200 scale (grids/A): 1.951326 object centre (A): 22.44900 14.89300 3.844001 number of atom coordinates read : 1959 total number of charged atoms : 1826 net assigned charge : 4.681008 assigned positive charge : 286.9501 centred at (gu) : 97.23924 88.25205 89.87406 assigned negative charge : -282.2693 centred at (gu) : 97.63209 87.85091 89.64693 start vw surface at 0.1500000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 61077 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17498 grid for indexing accessible points = 1.400000 m= 22161 mr = 42039 m= 3195 mr = 16731 m= 178 mr = 2055 m= 1 mr = 64 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5900000 number of dielectric boundary points 25723 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 158 iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 14439 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) : 0.6504421 object centre at (A) : 22.44900 14.89300 3.844001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.5049597E-02 2.1826347E-02 midg,1,midg; midg,igrid,midg 3.4199625E-03 1.1593482E-02 1,midg,midg; igrid,midg,midg 3.3009652E-02 -5.0527821E-03 gauss-seidel spectral radius is 0.9986213 estimated iterations to convergence 213 setup time was (sec) 0.9500000 now iterating at: 14:21:10 rms-change max change #iterations 3.663678 161.2086 at 10iterations 1.704607 64.59653 at 20iterations 0.7983008 29.14192 at 30iterations 0.3717997 12.68446 at 40iterations 0.1733015 6.359390 at 50iterations 8.0631554E-02 2.644470 at 60iterations 3.7679683E-02 1.238554 at 70iterations 1.7595658E-02 0.5962397 at 80iterations 8.1917914E-03 0.2654606 at 90iterations 3.8220054E-03 0.1274924 at 100iterations 1.7806188E-03 5.7922363E-02 at 110iterations 8.2805811E-04 3.5923541E-02 at 120iterations finished qdiffx linear iterations at : 14:21:20 total time elapsed so far: 10.64000 # loops : 120 mean,max change (kT/e) : 8.2805811E-04 3.5923541E-02 energy calculations done at 10.64000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.82000 DelPhi exited at 14:21:22 10.824u 0.562s 0:13.28 85.6% 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 Wed Dec 21 2011 at 14:21:23 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: 239 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1959 !!! WARNING: ASH 125 has a net charge of -0.3190 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.926990 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): -3.617000 48.51500 ymin,ymax (A): -4.999000 34.78500 zmin,zma (A): -23.52200 31.21000 x,y,z range (A): 52.13200 39.78400 54.73200 scale (grids/A): 2.926990 object centre (A): 22.44900 14.89300 3.844001 number of atom coordinates read : 1959 total number of charged atoms : 1826 net assigned charge : 4.681008 assigned positive charge : 286.9501 centred at (gu) : 100.8590 87.37809 89.81106 assigned negative charge : -282.2693 centred at (gu) : 101.4481 86.77650 89.47055 start vw surface at 0.1300000 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 141062 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17498 grid for indexing accessible points = 1.400000 m= 71558 mr = 101680 m= 25651 mr = 59240 m= 5706 mr = 21035 m= 790 mr = 4344 m= 50 mr = 555 m= 2 mr = 26 m= 0 mr = 0 time to grow re-entrant surface = 0.8400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.450000 number of dielectric boundary points 57939 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.620000 number of grid points assigned charge 14608 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) : 1.951326 object centre at (A) : 22.44900 14.89300 3.844001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.9386641 5.5890225E-02 midg,1,midg; midg,igrid,midg 8.8832557E-02 7.3656507E-02 1,midg,midg; igrid,midg,midg 0.2932063 -0.1027334 gauss-seidel spectral radius is 0.9992425 estimated iterations to convergence 287 setup time was (sec) 1.870000 now iterating at: 14:21:26 rms-change max change #iterations 8.680677 384.2272 at 10iterations 5.024475 145.8939 at 20iterations 2.884515 64.61972 at 30iterations 1.650889 35.69942 at 40iterations 0.9441758 19.97930 at 50iterations 0.5391682 10.86982 at 60iterations 0.3086964 6.258179 at 70iterations 0.1762166 3.362119 at 80iterations 0.1003071 1.992660 at 90iterations 5.7312600E-02 1.108545 at 100iterations 3.2631215E-02 0.6701927 at 110iterations 1.8624334E-02 0.3622408 at 120iterations 1.0610449E-02 0.2031603 at 130iterations 6.0446425E-03 0.1186573 at 140iterations 3.4420690E-03 7.7493668E-02 at 150iterations 1.9658618E-03 4.0039063E-02 at 160iterations 1.1179514E-03 2.1943569E-02 at 170iterations 6.3787936E-04 1.2880325E-02 at 180iterations finished qdiffx linear iterations at : 14:21:43 total time elapsed so far: 19.32000 # loops : 180 mean,max change (kT/e) : 6.3787936E-04 1.2880325E-02 energy calculations done at 19.32000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.51000 DelPhi exited at 14:21:45 19.507u 0.597s 0:22.39 89.7% 0+0k 0+0io 0pf+0w