Tue Oct 11 05:27:28 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 Tue Oct 11 2011 at 05:27:28 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: 281 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2008 !!! WARNING: SEP 190 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7506748 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): -2.779000 44.64500 ymin,ymax (A): -22.07100 24.41500 zmin,zma (A): 5.525000 48.30300 x,y,z range (A): 47.42400 46.48600 42.77800 scale (grids/A): 0.7506748 object centre (A): 20.93300 1.172000 26.91400 number of atom coordinates read : 2008 total number of charged atoms : 1878 net assigned charge : 6.025006 assigned positive charge : 304.4801 centred at (gu) : 90.37357 88.84177 89.84532 assigned negative charge : -298.4552 centred at (gu) : 90.26690 88.98345 89.74231 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7956 nv = 96 ne = 84 npr = 39950 no. pairs analyzed = 39950 no. exposed pairs = 2433 no. arc points = 16814 no. surface atoms = 827 nbur = 1181 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 589 mr = 4669 m= 6 mr = 135 m= 0 mr = 0 time to grow re-entrant surface = 9.0000018E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2700000 number of dielectric boundary points 3747 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1470 ## 142 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 8124 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.0008374E-09 2.4374626E-07 midg,1,midg; midg,igrid,midg 3.6581798E-07 -2.8616144E-08 1,midg,midg; igrid,midg,midg 4.8500137E-09 2.7307857E-07 gauss-seidel spectral radius is 0.9907365 estimated iterations to convergence 84 setup time was (sec) 0.5100000 now iterating at: 05:27:29 rms-change max change #iterations 0.2563386 37.43052 at 10iterations 3.6329839E-02 5.126987 at 20iterations 5.3215711E-03 0.6973782 at 30iterations 9.0192445E-04 0.1109219 at 40iterations 2.1649143E-04 2.0841599E-02 at 50iterations finished qdiffx linear iterations at : 05:27:32 total time elapsed so far: 3.110000 # loops : 50 mean,max change (kT/e) : 2.1649143E-04 2.0841599E-02 energy calculations done at 3.110000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.280000 DelPhi exited at 05:27:32 3.287u 0.177s 0:04.05 85.1% 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 05:27:32 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: 281 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2008 !!! WARNING: SEP 190 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.252024 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): -2.779000 44.64500 ymin,ymax (A): -22.07100 24.41500 zmin,zma (A): 5.525000 48.30300 x,y,z range (A): 47.42400 46.48600 42.77800 scale (grids/A): 2.252024 object centre (A): 20.93300 1.172000 26.91400 number of atom coordinates read : 2008 total number of charged atoms : 1878 net assigned charge : 6.025006 assigned positive charge : 304.4801 centred at (gu) : 91.12071 86.52543 89.53605 assigned negative charge : -298.4552 centred at (gu) : 90.80074 86.95029 89.22702 start vw surface at 0.1400000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 83393 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16814 grid for indexing accessible points = 1.400000 m= 36324 mr = 59977 m= 8116 mr = 28399 m= 921 mr = 5683 m= 40 mr = 521 m= 0 mr = 12 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6200000 number of dielectric boundary points 34202 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 44 iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 14974 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) : 0.7506748 object centre at (A) : 20.93300 1.172000 26.91400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.8739209E-02 3.4955252E-02 midg,1,midg; midg,igrid,midg 5.2046590E-02 -6.0322434E-02 1,midg,midg; igrid,midg,midg 6.9175646E-02 0.1030340 gauss-seidel spectral radius is 0.9989393 estimated iterations to convergence 243 setup time was (sec) 0.9000000 now iterating at: 05:27:33 rms-change max change #iterations 5.014982 172.6096 at 10iterations 2.578404 87.94302 at 20iterations 1.320825 45.64449 at 30iterations 0.6802650 20.83065 at 40iterations 0.3501970 9.804276 at 50iterations 0.1796421 5.022362 at 60iterations 9.2356123E-02 2.531548 at 70iterations 4.7386359E-02 1.304273 at 80iterations 2.4498660E-02 0.7045116 at 90iterations 1.2788145E-02 0.3464327 at 100iterations 6.6923578E-03 0.1923227 at 110iterations 3.5775614E-03 0.1022549 at 120iterations finished qdiffx linear iterations at : 05:27:40 total time elapsed so far: 7.380000 # loops : 120 mean,max change (kT/e) : 3.5775614E-03 0.1022549 energy calculations done at 7.380000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.550000 DelPhi exited at 05:27:41 7.554u 0.231s 0:08.33 93.3% 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 05:27:41 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: 281 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2008 !!! WARNING: SEP 190 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.378036 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): -2.779000 44.64500 ymin,ymax (A): -22.07100 24.41500 zmin,zma (A): 5.525000 48.30300 x,y,z range (A): 47.42400 46.48600 42.77800 scale (grids/A): 3.378036 object centre (A): 20.93300 1.172000 26.91400 number of atom coordinates read : 2008 total number of charged atoms : 1878 net assigned charge : 6.025006 assigned positive charge : 304.4801 centred at (gu) : 91.68130 84.78825 89.30412 assigned negative charge : -298.4552 centred at (gu) : 91.20117 85.42548 88.84046 start vw surface at 0.1400000 fill in re-entrant regions at 0.8700000 boundary points on vw surface= 191808 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16814 grid for indexing accessible points = 1.400000 m= 109570 mr = 143696 m= 49145 mr = 92660 m= 15889 mr = 41380 m= 3665 mr = 12605 m= 561 mr = 2751 m= 40 mr = 394 m= 1 mr = 18 m= 0 mr = 0 time to grow re-entrant surface = 1.010000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.010000 number of dielectric boundary points 77175 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.160000 number of grid points assigned charge 15024 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) : 2.252024 object centre at (A) : 20.93300 1.172000 26.91400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1736705 0.1951486 midg,1,midg; midg,igrid,midg 0.4974076 -0.6020761 1,midg,midg; igrid,midg,midg 0.4572459 0.7057130 gauss-seidel spectral radius is 0.9993255 estimated iterations to convergence 304 setup time was (sec) 2.340000 now iterating at: 05:27:43 rms-change max change #iterations 10.86242 253.7763 at 10iterations 6.537971 136.2133 at 20iterations 3.908311 67.88835 at 30iterations 2.331139 43.45526 at 40iterations 1.388640 24.80054 at 50iterations 0.8252375 13.77954 at 60iterations 0.4904658 9.163155 at 70iterations 0.2912111 4.894794 at 80iterations 0.1729261 2.928097 at 90iterations 0.1027480 1.631599 at 100iterations 6.1101392E-02 1.111797 at 110iterations 3.6537062E-02 0.6604462 at 120iterations 2.2122663E-02 0.3892517 at 130iterations 1.3635712E-02 0.2462931 at 140iterations 8.6969594E-03 0.1544590 at 150iterations 5.8279531E-03 0.1059036 at 160iterations 4.1262270E-03 8.3786011E-02 at 170iterations 3.0983449E-03 5.6327820E-02 at 180iterations finished qdiffx linear iterations at : 05:27:53 total time elapsed so far: 12.05000 # loops : 180 mean,max change (kT/e) : 3.0983449E-03 5.6327820E-02 energy calculations done at 12.05000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.24000 DelPhi exited at 05:27:53 12.238u 0.197s 0:12.74 97.4% 0+0k 0+0io 0pf+0w