Wed Dec 28 11:02:49 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+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 Wed Dec 28 2011 at 11:02:49 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1966 !!! WARNING: ASH 25 has a net charge of -0.3190 !!! 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: 0.6489601 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): -6.208000 34.52000 ymin,ymax (A): -3.531000 48.00500 zmin,zma (A): -23.98100 30.87600 x,y,z range (A): 40.72800 51.53600 54.85700 scale (grids/A): 0.6489601 object centre (A): 14.15600 22.23700 3.447500 number of atom coordinates read : 1966 total number of charged atoms : 1832 net assigned charge : 3.362005 assigned positive charge : 292.6019 centred at (gu) : 90.91563 92.55228 90.13947 assigned negative charge : -289.2403 centred at (gu) : 91.03268 92.70315 90.07806 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 5579 nv = 96 ne = 84 npr = 40609 no. pairs analyzed = 40609 no. exposed pairs = 2416 no. arc points = 16981 no. surface atoms = 820 nbur = 1146 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 292 mr = 3137 m= 2 mr = 43 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 51 time to turn everything in is 0.2900000 number of dielectric boundary points 2693 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1665 ## 165 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 6579 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.1314078E-10 1.3966225E-08 midg,1,midg; midg,igrid,midg 1.3577411E-08 -1.7705744E-08 1,midg,midg; igrid,midg,midg 1.6117420E-08 -7.5347684E-09 gauss-seidel spectral radius is 0.9876371 estimated iterations to convergence 73 setup time was (sec) 0.7600000 now iterating at: 11:02:50 rms-change max change #iterations 0.1369261 21.82360 at 10iterations 1.3911361E-02 2.591030 at 20iterations 1.4092796E-03 0.2146413 at 30iterations 1.4321311E-04 2.1198273E-02 at 40iterations 1.4819128E-05 2.1133423E-03 at 50iterations finished qdiffx linear iterations at : 11:02:57 total time elapsed so far: 6.690000 # loops : 50 mean,max change (kT/e) : 1.4819128E-05 2.1133423E-03 energy calculations done at 6.690000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.880000 DelPhi exited at 11:02:57 6.886u 0.765s 0:08.21 93.0% 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 28 2011 at 11:02:57 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1966 !!! WARNING: ASH 25 has a net charge of -0.3190 !!! 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: 1.946880 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): -6.208000 34.52000 ymin,ymax (A): -3.531000 48.00500 zmin,zma (A): -23.98100 30.87600 x,y,z range (A): 40.72800 51.53600 54.85700 scale (grids/A): 1.946880 object centre (A): 14.15600 22.23700 3.447500 number of atom coordinates read : 1966 total number of charged atoms : 1832 net assigned charge : 3.362005 assigned positive charge : 292.6019 centred at (gu) : 92.74689 97.65650 90.41848 assigned negative charge : -289.2403 centred at (gu) : 93.09811 98.10953 90.23450 start vw surface at 0.1200000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 60282 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16981 grid for indexing accessible points = 1.400000 m= 21981 mr = 41913 m= 3476 mr = 16775 m= 198 mr = 2307 m= 3 mr = 94 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 2029 time to turn everything in is 0.6200000 number of dielectric boundary points 24851 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 94 iepsmp to db, and charging done at 0.8200000 number of grid points assigned charge 14459 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) : 0.6489601 object centre at (A) : 14.15600 22.23700 3.447500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.9912723E-02 1.6892707E-02 midg,1,midg; midg,igrid,midg 3.8059462E-02 -1.2486461E-02 1,midg,midg; igrid,midg,midg 1.1997575E-02 -4.0301546E-03 gauss-seidel spectral radius is 0.9986118 estimated iterations to convergence 213 setup time was (sec) 1.140000 now iterating at: 11:02:59 rms-change max change #iterations 3.793877 185.8219 at 10iterations 1.768881 61.68672 at 20iterations 0.8280112 30.13519 at 30iterations 0.3846187 13.88559 at 40iterations 0.1782503 6.723663 at 50iterations 8.3050966E-02 2.776737 at 60iterations 3.8557995E-02 1.302273 at 70iterations 1.8033097E-02 0.6461773 at 80iterations 8.3549889E-03 0.2772446 at 90iterations 3.8952241E-03 0.1255417 at 100iterations 1.8082728E-03 5.9360504E-02 at 110iterations 8.4385340E-04 2.8548241E-02 at 120iterations finished qdiffx linear iterations at : 11:03:15 total time elapsed so far: 17.16000 # loops : 120 mean,max change (kT/e) : 8.4385340E-04 2.8548241E-02 energy calculations done at 17.16000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.32000 DelPhi exited at 11:03:16 17.322u 1.002s 0:18.67 98.1% 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 Wed Dec 28 2011 at 11:03:16 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1966 !!! WARNING: ASH 25 has a net charge of -0.3190 !!! 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: 2.920320 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): -6.208000 34.52000 ymin,ymax (A): -3.531000 48.00500 zmin,zma (A): -23.98100 30.87600 x,y,z range (A): 40.72800 51.53600 54.85700 scale (grids/A): 2.920320 object centre (A): 14.15600 22.23700 3.447500 number of atom coordinates read : 1966 total number of charged atoms : 1832 net assigned charge : 3.362005 assigned positive charge : 292.6019 centred at (gu) : 94.12034 101.4847 90.62749 assigned negative charge : -289.2403 centred at (gu) : 94.64730 102.1643 90.35179 start vw surface at 0.1200000 fill in re-entrant regions at 0.5200000 boundary points on vw surface= 139535 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16981 grid for indexing accessible points = 1.400000 m= 70987 mr = 101342 m= 26098 mr = 59170 m= 6234 mr = 21643 m= 970 mr = 4923 m= 62 mr = 662 m= 0 mr = 33 time to grow re-entrant surface = 0.8700000 no. cavity mid-points inaccessible to solvent = 6208 time to turn everything in is 1.550000 number of dielectric boundary points 56113 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.840000 number of grid points assigned charge 14655 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) : 1.946880 object centre at (A) : 14.15600 22.23700 3.447500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.8934861 4.7076516E-02 midg,1,midg; midg,igrid,midg 0.3679623 -0.1526406 1,midg,midg; igrid,midg,midg 9.1407128E-02 -1.0400916E-02 gauss-seidel spectral radius is 0.9992386 estimated iterations to convergence 286 setup time was (sec) 2.190000 now iterating at: 11:03:19 rms-change max change #iterations 8.823790 465.7310 at 10iterations 5.056059 116.4787 at 20iterations 2.868641 55.94985 at 30iterations 1.633430 35.35777 at 40iterations 0.9289817 22.49006 at 50iterations 0.5290756 11.98314 at 60iterations 0.3008172 5.939515 at 70iterations 0.1706554 3.262840 at 80iterations 9.7117417E-02 2.122476 at 90iterations 5.5253383E-02 1.083099 at 100iterations 3.1372424E-02 0.6248901 at 110iterations 1.7838657E-02 0.3629141 at 120iterations 1.0158809E-02 0.1935005 at 130iterations 5.7580001E-03 0.1149712 at 140iterations 3.2825849E-03 6.9550037E-02 at 150iterations 1.8637591E-03 3.6496162E-02 at 160iterations 1.0632040E-03 2.0011902E-02 at 170iterations 6.0461205E-04 1.2119293E-02 at 180iterations finished qdiffx linear iterations at : 11:03:47 total time elapsed so far: 29.50000 # loops : 180 mean,max change (kT/e) : 6.0461205E-04 1.2119293E-02 energy calculations done at 29.50000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 29.67000 DelPhi exited at 11:03:47 29.677u 1.019s 0:31.43 97.6% 0+0k 0+0io 0pf+0w