Tue Oct 11 03:24:57 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 Tue Oct 11 2011 at 03:24:57 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2532 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: 0.5715386 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): -14.62700 38.81700 ymin,ymax (A): -24.28100 38.00700 zmin,zma (A): -15.23900 34.52000 x,y,z range (A): 53.44400 62.28800 49.75900 scale (grids/A): 0.5715386 object centre (A): 12.09500 6.863000 9.640499 number of atom coordinates read : 2532 total number of charged atoms : 2388 net assigned charge : 7.500025 assigned positive charge : 381.2031 centred at (gu) : 87.91866 88.67434 90.26647 assigned negative charge : -373.7037 centred at (gu) : 87.86487 88.71545 90.25537 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 5300 nv = 96 ne = 84 npr = 51146 no. pairs analyzed = 51146 no. exposed pairs = 3295 no. arc points = 23007 no. surface atoms = 1100 nbur = 1432 mkacc time = 9.0000004E-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= 247 mr = 2658 m= 1 mr = 24 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 16 time to turn everything in is 0.1900000 number of dielectric boundary points 2866 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2329 ## 252 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 6878 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.9962905E-10 1.4561216E-09 midg,1,midg; midg,igrid,midg 2.4337481E-09 4.8294502E-10 1,midg,midg; igrid,midg,midg 7.2810352E-10 1.2074057E-09 gauss-seidel spectral radius is 0.9841661 estimated iterations to convergence 65 setup time was (sec) 0.3800000 now iterating at: 03:24:57 rms-change max change #iterations 8.5731559E-02 14.36538 at 10iterations 6.3922582E-03 1.052753 at 20iterations 4.8443506E-04 7.7651978E-02 at 30iterations 4.0719413E-05 7.0266724E-03 at 40iterations 4.8029424E-06 9.4890594E-04 at 50iterations finished qdiffx linear iterations at : 03:25:00 total time elapsed so far: 3.250000 # loops : 50 mean,max change (kT/e) : 4.8029424E-06 9.4890594E-04 energy calculations done at 3.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.380000 DelPhi exited at 03:25:01 3.387u 0.178s 0:03.94 90.1% 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 Oct 11 2011 at 03:25:01 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2532 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.714616 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): -14.62700 38.81700 ymin,ymax (A): -24.28100 38.00700 zmin,zma (A): -15.23900 34.52000 x,y,z range (A): 53.44400 62.28800 49.75900 scale (grids/A): 1.714616 object centre (A): 12.09500 6.863000 9.640499 number of atom coordinates read : 2532 total number of charged atoms : 2388 net assigned charge : 7.500025 assigned positive charge : 381.2031 centred at (gu) : 83.75562 86.02265 90.79888 assigned negative charge : -373.7037 centred at (gu) : 83.59445 86.14617 90.76587 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 58119 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23007 grid for indexing accessible points = 1.400000 m= 18600 mr = 38575 m= 2303 mr = 12772 m= 86 mr = 1215 m= 1 mr = 10 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 405 time to turn everything in is 0.2900000 number of dielectric boundary points 26537 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 236 iepsmp to db, and charging done at 0.3500000 number of grid points assigned charge 18425 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) : 0.5715386 object centre at (A) : 12.09500 6.863000 9.640499 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.5252672E-03 9.3401587E-03 midg,1,midg; midg,igrid,midg 8.7885419E-03 -9.8697552E-03 1,midg,midg; igrid,midg,midg 8.6498400E-03 -4.8566799E-04 gauss-seidel spectral radius is 0.9983090 estimated iterations to convergence 193 setup time was (sec) 0.4900000 now iterating at: 03:25:01 rms-change max change #iterations 3.357523 146.8080 at 10iterations 1.435504 59.27219 at 20iterations 0.6173152 25.92781 at 30iterations 0.2650544 10.48089 at 40iterations 0.1137975 4.640160 at 50iterations 4.8731521E-02 2.010262 at 60iterations 2.0984711E-02 0.8025742 at 70iterations 9.0364488E-03 0.3771019 at 80iterations 3.8713033E-03 0.1406021 at 90iterations 1.6685210E-03 6.3556671E-02 at 100iterations 7.1616261E-04 2.8125763E-02 at 110iterations 3.0825596E-04 1.2748241E-02 at 120iterations finished qdiffx linear iterations at : 03:25:08 total time elapsed so far: 7.400000 # loops : 120 mean,max change (kT/e) : 3.0825596E-04 1.2748241E-02 energy calculations done at 7.400000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.540000 DelPhi exited at 03:25:09 7.540u 0.212s 0:08.29 93.4% 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 Oct 11 2011 at 03:25:09 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2532 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.571924 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): -14.62700 38.81700 ymin,ymax (A): -24.28100 38.00700 zmin,zma (A): -15.23900 34.52000 x,y,z range (A): 53.44400 62.28800 49.75900 scale (grids/A): 2.571924 object centre (A): 12.09500 6.863000 9.640499 number of atom coordinates read : 2532 total number of charged atoms : 2388 net assigned charge : 7.500025 assigned positive charge : 381.2031 centred at (gu) : 80.63326 84.03378 91.19809 assigned negative charge : -373.7037 centred at (gu) : 80.39161 84.21925 91.14880 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 134865 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23007 grid for indexing accessible points = 1.400000 m= 62519 mr = 94520 m= 19627 mr = 48974 m= 3959 mr = 14987 m= 337 mr = 2754 m= 11 mr = 149 m= 0 mr = 0 time to grow re-entrant surface = 0.3900000 no. cavity mid-points inaccessible to solvent = 1293 time to turn everything in is 0.7100000 number of dielectric boundary points 59934 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 9 iepsmp to db, and charging done at 0.8000000 number of grid points assigned charge 19092 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) : 1.714616 object centre at (A) : 12.09500 6.863000 9.640499 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.5033991E-03 0.1043580 midg,1,midg; midg,igrid,midg 9.4932355E-02 -0.2620952 1,midg,midg; igrid,midg,midg 0.1044023 -5.1562060E-02 gauss-seidel spectral radius is 0.9991669 estimated iterations to convergence 274 setup time was (sec) 0.9400000 now iterating at: 03:25:10 rms-change max change #iterations 8.462644 306.3038 at 10iterations 4.815203 112.3806 at 20iterations 2.724769 66.39693 at 30iterations 1.534146 34.45443 at 40iterations 0.8595523 19.70293 at 50iterations 0.4802260 12.09499 at 60iterations 0.2685872 6.297606 at 70iterations 0.1500501 3.400906 at 80iterations 8.3581947E-02 1.846478 at 90iterations 4.6527892E-02 1.051960 at 100iterations 2.5895482E-02 0.6450386 at 110iterations 1.4380491E-02 0.3116798 at 120iterations 8.0044037E-03 0.1671524 at 130iterations 4.4509307E-03 9.3791008E-02 at 140iterations 2.4654137E-03 5.2722931E-02 at 150iterations 1.3703603E-03 2.9027939E-02 at 160iterations 7.6290022E-04 1.5878677E-02 at 170iterations 4.2417127E-04 1.0177612E-02 at 180iterations finished qdiffx linear iterations at : 03:25:21 total time elapsed so far: 11.94000 # loops : 180 mean,max change (kT/e) : 4.2417127E-04 1.0177612E-02 energy calculations done at 11.94000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.07000 DelPhi exited at 03:25:22 12.071u 0.214s 0:12.75 96.3% 0+0k 0+0io 0pf+0w