Mon Oct 10 14:38:00 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 14:38:00 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2731 !!! WARNING: ADP 662 has a net charge of -2.0000 !!! WARNING: MG6 664 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5918832 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): -7.958000 52.18900 ymin,ymax (A): -16.17900 34.45800 zmin,zma (A): 77.42900 129.9400 x,y,z range (A): 60.14700 50.63700 52.51100 scale (grids/A): 0.5918832 object centre (A): 22.11550 9.139500 103.6845 number of atom coordinates read : 2731 total number of charged atoms : 2589 net assigned charge : -3.599991 assigned positive charge : 426.1494 centred at (gu) : 91.96021 89.64542 89.45045 assigned negative charge : -429.7503 centred at (gu) : 91.89446 89.73315 89.52078 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6348 nv = 96 ne = 84 npr = 54066 no. pairs analyzed = 54066 no. exposed pairs = 3672 no. arc points = 25444 no. surface atoms = 1232 nbur = 1499 mkacc time = 8.9999996E-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 = 1.484000 m= 331 mr = 3269 m= 1 mr = 33 m= 0 mr = 0 time to grow re-entrant surface = 9.9999987E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2100000 number of dielectric boundary points 3378 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2581 ## 282 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 7949 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0709453E-09 -3.0434948E-09 midg,1,midg; midg,igrid,midg 1.5989060E-09 -3.6911587E-09 1,midg,midg; igrid,midg,midg -2.1181497E-09 1.3051457E-09 gauss-seidel spectral radius is 0.9852448 estimated iterations to convergence 68 setup time was (sec) 0.3900000 now iterating at: 14:38:01 rms-change max change #iterations 0.1101006 16.26687 at 10iterations 9.1817547E-03 1.353657 at 20iterations 7.7209418E-04 0.1425037 at 30iterations 8.8453497E-05 1.3750076E-02 at 40iterations 1.6852820E-05 2.5911331E-03 at 50iterations finished qdiffx linear iterations at : 14:38:04 total time elapsed so far: 3.210000 # loops : 50 mean,max change (kT/e) : 1.6852820E-05 2.5911331E-03 energy calculations done at 3.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.340000 DelPhi exited at 14:38:04 3.344u 0.193s 0:04.31 81.9% 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 14:38:05 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2731 !!! WARNING: ADP 662 has a net charge of -2.0000 !!! WARNING: MG6 664 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.775650 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): -7.958000 52.18900 ymin,ymax (A): -16.17900 34.45800 zmin,zma (A): 77.42900 129.9400 x,y,z range (A): 60.14700 50.63700 52.51100 scale (grids/A): 1.775650 object centre (A): 22.11550 9.139500 103.6845 number of atom coordinates read : 2731 total number of charged atoms : 2589 net assigned charge : -3.599991 assigned positive charge : 426.1494 centred at (gu) : 95.88000 88.93571 88.35045 assigned negative charge : -429.7503 centred at (gu) : 95.68288 89.19923 88.56213 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 69131 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25444 grid for indexing accessible points = 1.400000 m= 23215 mr = 46424 m= 3164 mr = 16150 m= 156 mr = 1695 m= 1 mr = 27 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3400000 number of dielectric boundary points 31371 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 220 iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 20183 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) : 0.5918832 object centre at (A) : 22.11550 9.139500 103.6845 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.7364038E-03 -3.0271091E-02 midg,1,midg; midg,igrid,midg -7.1411678E-03 -1.7975284E-02 1,midg,midg; igrid,midg,midg 1.8443115E-02 3.1800508E-02 gauss-seidel spectral radius is 0.9984558 estimated iterations to convergence 202 setup time was (sec) 0.5400000 now iterating at: 14:38:05 rms-change max change #iterations 3.976590 192.0709 at 10iterations 1.768523 60.06520 at 20iterations 0.7852017 27.44598 at 30iterations 0.3507027 12.47925 at 40iterations 0.1561448 5.902227 at 50iterations 6.9901340E-02 2.542568 at 60iterations 3.1099642E-02 1.025797 at 70iterations 1.3851435E-02 0.4749756 at 80iterations 6.1953487E-03 0.2050934 at 90iterations 2.7916594E-03 9.3669891E-02 at 100iterations 1.2528951E-03 4.3332219E-02 at 110iterations 5.6926982E-04 1.9242287E-02 at 120iterations finished qdiffx linear iterations at : 14:38:12 total time elapsed so far: 7.440000 # loops : 120 mean,max change (kT/e) : 5.6926982E-04 1.9242287E-02 energy calculations done at 7.440000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.570000 DelPhi exited at 14:38:13 7.568u 0.198s 0:08.22 94.2% 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 Mon Oct 10 2011 at 14:38:13 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2731 !!! WARNING: ADP 662 has a net charge of -2.0000 !!! WARNING: MG6 664 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.663474 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): -7.958000 52.18900 ymin,ymax (A): -16.17900 34.45800 zmin,zma (A): 77.42900 129.9400 x,y,z range (A): 60.14700 50.63700 52.51100 scale (grids/A): 2.663474 object centre (A): 22.11550 9.139500 103.6845 number of atom coordinates read : 2731 total number of charged atoms : 2589 net assigned charge : -3.599991 assigned positive charge : 426.1494 centred at (gu) : 98.81985 88.40340 87.52560 assigned negative charge : -429.7503 centred at (gu) : 98.52420 88.79877 87.84305 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 160122 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25444 grid for indexing accessible points = 1.400000 m= 76958 mr = 113526 m= 25377 mr = 60544 m= 5330 mr = 19447 m= 607 mr = 3691 m= 14 mr = 331 m= 0 mr = 0 time to grow re-entrant surface = 0.4900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8600000 number of dielectric boundary points 70869 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 8 iepsmp to db, and charging done at 0.9400000 number of grid points assigned charge 20706 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) : 1.775650 object centre at (A) : 22.11550 9.139500 103.6845 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1054765 -0.3939959 midg,1,midg; midg,igrid,midg -0.1113064 -0.1888407 1,midg,midg; igrid,midg,midg 0.3700137 0.3088860 gauss-seidel spectral radius is 0.9992165 estimated iterations to convergence 282 setup time was (sec) 1.080000 now iterating at: 14:38:14 rms-change max change #iterations 9.794707 314.9764 at 10iterations 5.673075 131.4899 at 20iterations 3.257094 66.08445 at 30iterations 1.863150 40.26203 at 40iterations 1.061578 23.83676 at 50iterations 0.6038802 13.12183 at 60iterations 0.3431676 7.489453 at 70iterations 0.1949403 4.059544 at 80iterations 0.1104047 2.250904 at 90iterations 6.2400497E-02 1.301579 at 100iterations 3.5387516E-02 0.7232904 at 110iterations 2.0008288E-02 0.3869896 at 120iterations 1.1316259E-02 0.2157955 at 130iterations 6.4024604E-03 0.1351080 at 140iterations 3.6267524E-03 6.8008423E-02 at 150iterations 2.0520606E-03 3.8802147E-02 at 160iterations 1.1629517E-03 2.2836685E-02 at 170iterations 6.6045229E-04 1.2317657E-02 at 180iterations finished qdiffx linear iterations at : 14:38:25 total time elapsed so far: 12.19000 # loops : 180 mean,max change (kT/e) : 6.6045229E-04 1.2317657E-02 energy calculations done at 12.19000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.32000 DelPhi exited at 14:38:26 12.326u 0.221s 0:13.22 94.8% 0+0k 0+0io 0pf+0w