Wed Feb 15 08:53:30 PST 2012 #!/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_thinner.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 Feb 15 2012 at 08:53:31 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2627 !!! WARNING: HID 94 has a net charge of 1.4000 !!! WARNING: HID 96 has a net charge of 1.4000 !!! WARNING: HIE 119 has a net charge of 1.4000 !!! WARNING: ZN5 501 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: 0.6284534 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): -31.83200 17.65800 ymin,ymax (A): -23.75800 22.22600 zmin,zma (A): -12.19800 44.44900 x,y,z range (A): 49.49000 45.98400 56.64700 scale (grids/A): 0.6284534 object centre (A): -7.086999 -0.7659998 16.12550 number of atom coordinates read : 2627 total number of charged atoms : 2454 net assigned charge : 8.100017 assigned positive charge : 394.6720 centred at (gu) : 88.46186 89.49805 89.89104 assigned negative charge : -386.5726 centred at (gu) : 88.36119 89.54732 89.79486 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6756 nv = 96 ne = 84 npr = 56064 no. pairs analyzed = 56064 no. exposed pairs = 3040 no. arc points = 21472 no. surface atoms = 1022 nbur = 1605 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 353 mr = 3832 m= 1 mr = 60 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 169 time to turn everything in is 0.2000000 number of dielectric boundary points 3218 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2091 ## 196 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 8224 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.5695175E-10 1.6153876E-08 midg,1,midg; midg,igrid,midg 1.4096298E-08 3.9539851E-09 1,midg,midg; igrid,midg,midg -2.5803254E-10 1.2166768E-08 gauss-seidel spectral radius is 0.9868819 estimated iterations to convergence 71 setup time was (sec) 0.4300000 now iterating at: 08:53:31 rms-change max change #iterations 0.1467895 25.28689 at 10iterations 1.3853031E-02 2.022568 at 20iterations 1.3406193E-03 0.2022552 at 30iterations 1.2597370E-04 1.8712997E-02 at 40iterations 1.2277987E-05 1.8005371E-03 at 50iterations finished qdiffx linear iterations at : 08:53:35 total time elapsed so far: 3.820000 # loops : 50 mean,max change (kT/e) : 1.2277987E-05 1.8005371E-03 energy calculations done at 3.820000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.950000 DelPhi exited at 08:53:35 3.956u 0.238s 0:04.89 85.4% 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 Wed Feb 15 2012 at 08:53:36 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2627 !!! WARNING: HID 94 has a net charge of 1.4000 !!! WARNING: HID 96 has a net charge of 1.4000 !!! WARNING: HIE 119 has a net charge of 1.4000 !!! WARNING: ZN5 501 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: 1.885360 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): -31.83200 17.65800 ymin,ymax (A): -23.75800 22.22600 zmin,zma (A): -12.19800 44.44900 x,y,z range (A): 49.49000 45.98400 56.64700 scale (grids/A): 1.885360 object centre (A): -7.086999 -0.7659998 16.12550 number of atom coordinates read : 2627 total number of charged atoms : 2454 net assigned charge : 8.100017 assigned positive charge : 394.6720 centred at (gu) : 85.38507 88.49387 89.67251 assigned negative charge : -386.5726 centred at (gu) : 85.08337 88.64182 89.38428 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 73205 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21472 grid for indexing accessible points = 1.400000 m= 26239 mr = 51538 m= 3833 mr = 19689 m= 229 mr = 2446 m= 0 mr = 92 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 7763 time to turn everything in is 0.3800000 number of dielectric boundary points 29741 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 136 iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 19268 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) : 0.6284534 object centre at (A) : -7.086999 -0.7659998 16.12550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.1226648E-02 3.8853269E-02 midg,1,midg; midg,igrid,midg 2.2196343E-02 3.7285627E-03 1,midg,midg; igrid,midg,midg 7.3730159E-03 4.2518564E-02 gauss-seidel spectral radius is 0.9986028 estimated iterations to convergence 212 setup time was (sec) 0.6600000 now iterating at: 08:53:37 rms-change max change #iterations 4.184247 179.7088 at 10iterations 1.943643 62.61786 at 20iterations 0.9013318 29.17035 at 30iterations 0.4168044 14.38072 at 40iterations 0.1934358 5.981564 at 50iterations 9.0040021E-02 2.924820 at 60iterations 4.1749049E-02 1.396931 at 70iterations 1.9472785E-02 0.6281273 at 80iterations 9.0218792E-03 0.2870274 at 90iterations 4.2015216E-03 0.1298370 at 100iterations 1.9519875E-03 6.3793182E-02 at 110iterations 9.0625510E-04 2.9085159E-02 at 120iterations finished qdiffx linear iterations at : 08:53:45 total time elapsed so far: 8.680000 # loops : 120 mean,max change (kT/e) : 9.0625510E-04 2.9085159E-02 energy calculations done at 8.680000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.820000 DelPhi exited at 08:53:45 8.820u 0.268s 0:09.97 91.0% 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 Feb 15 2012 at 08:53:46 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2627 !!! WARNING: HID 94 has a net charge of 1.4000 !!! WARNING: HID 96 has a net charge of 1.4000 !!! WARNING: HIE 119 has a net charge of 1.4000 !!! WARNING: ZN5 501 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: 2.828040 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): -31.83200 17.65800 ymin,ymax (A): -23.75800 22.22600 zmin,zma (A): -12.19800 44.44900 x,y,z range (A): 49.49000 45.98400 56.64700 scale (grids/A): 2.828040 object centre (A): -7.086999 -0.7659998 16.12550 number of atom coordinates read : 2627 total number of charged atoms : 2454 net assigned charge : 8.100017 assigned positive charge : 394.6720 centred at (gu) : 83.07746 87.74081 89.50857 assigned negative charge : -386.5726 centred at (gu) : 82.62497 87.96262 89.07638 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 169115 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21472 grid for indexing accessible points = 1.400000 m= 85811 mr = 124166 m= 30374 mr = 71136 m= 6820 mr = 24830 m= 969 mr = 5288 m= 57 mr = 702 m= 0 mr = 20 time to grow re-entrant surface = 0.5300000 no. cavity mid-points inaccessible to solvent = 26087 time to turn everything in is 0.9600000 number of dielectric boundary points 67004 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.080000 number of grid points assigned charge 19630 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) : 1.885360 object centre at (A) : -7.086999 -0.7659998 16.12550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.9714316E-02 0.4303686 midg,1,midg; midg,igrid,midg 0.2513565 6.7682513E-03 1,midg,midg; igrid,midg,midg 0.1228874 0.5181727 gauss-seidel spectral radius is 0.9992427 estimated iterations to convergence 287 setup time was (sec) 1.260000 now iterating at: 08:53:47 rms-change max change #iterations 9.726999 334.4154 at 10iterations 5.588117 153.6518 at 20iterations 3.186992 58.92373 at 30iterations 1.820447 35.52498 at 40iterations 1.041452 18.94222 at 50iterations 0.5927207 10.72937 at 60iterations 0.3386935 6.388565 at 70iterations 0.1934257 3.460834 at 80iterations 0.1102563 2.038933 at 90iterations 6.2737621E-02 1.176502 at 100iterations 3.5814207E-02 0.7317009 at 110iterations 2.0415841E-02 0.3508682 at 120iterations 1.1688312E-02 0.2042437 at 130iterations 6.6607338E-03 0.1253510 at 140iterations 3.7960366E-03 6.9307327E-02 at 150iterations 2.1652535E-03 3.9949417E-02 at 160iterations 1.2308866E-03 2.2167206E-02 at 170iterations 7.0471788E-04 1.2205124E-02 at 180iterations finished qdiffx linear iterations at : 08:54:00 total time elapsed so far: 14.24000 # loops : 180 mean,max change (kT/e) : 7.0471788E-04 1.2205124E-02 energy calculations done at 14.24000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.37000 DelPhi exited at 08:54:01 14.368u 0.311s 0:15.07 97.3% 0+0k 0+0io 0pf+0w