Mon Oct 10 17:07:43 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 17:07:43 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: 349 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4344 !!! WARNING: GLM 182 has a net charge of -0.0940 !!! WARNING: HEM 841 has a net charge of -3.4000 !!! WARNING: FE 2 has a net charge of 1.4000 !!! WARNING: FE 3 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= 0.1200000 grid size : 179 scale,in grids/A, set to be: 0.5128427 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): -13.17200 41.81200 ymin,ymax (A): 24.36300 88.34900 zmin,zma (A): -3.543000 65.87400 x,y,z range (A): 54.98400 63.98600 69.41700 scale (grids/A): 0.5128427 object centre (A): 14.32000 56.35600 31.16550 number of atom coordinates read : 4344 total number of charged atoms : 4139 net assigned charge : 3.306056 assigned positive charge : 653.0941 centred at (gu) : 90.60685 88.99752 87.52361 assigned negative charge : -649.7921 centred at (gu) : 90.73674 88.99881 87.63825 start vw surface at 0.2000000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 7202 nv = 96 ne = 84 npr = 88271 no. pairs analyzed = 88271 no. exposed pairs = 5680 no. arc points = 39428 no. surface atoms = 1881 nbur = 2463 mkacc time = 0.1900000 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 = 1.652000 m= 268 mr = 3633 m= 0 mr = 6 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4500000 number of dielectric boundary points 3831 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3806 ## 527 charges are in solution ## iepsmp to db, and charging done at 0.5700000 number of grid points assigned charge 9681 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.5389266E-10 -1.3156125E-10 midg,1,midg; midg,igrid,midg 6.3396774E-11 3.2990440E-11 1,midg,midg; igrid,midg,midg 3.1878900E-10 -3.4655465E-10 gauss-seidel spectral radius is 0.9805250 estimated iterations to convergence 59 setup time was (sec) 0.7000000 now iterating at: 17:07:44 rms-change max change #iterations 6.7415297E-02 9.909916 at 10iterations 4.1962527E-03 0.6311703 at 20iterations 8.5571629E-04 0.1407461 at 30iterations 4.2887012E-04 7.0581436E-02 at 40iterations 2.2279365E-04 3.6018372E-02 at 50iterations finished qdiffx linear iterations at : 17:07:47 total time elapsed so far: 3.430000 # loops : 50 mean,max change (kT/e) : 2.2279365E-04 3.6018372E-02 energy calculations done at 3.430000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.600000 DelPhi exited at 17:07:47 3.604u 0.241s 0:04.19 91.6% 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 17:07:48 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: 349 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4344 !!! WARNING: GLM 182 has a net charge of -0.0940 !!! WARNING: HEM 841 has a net charge of -3.4000 !!! WARNING: FE 2 has a net charge of 1.4000 !!! WARNING: FE 3 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= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.538528 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): -13.17200 41.81200 ymin,ymax (A): 24.36300 88.34900 zmin,zma (A): -3.543000 65.87400 x,y,z range (A): 54.98400 63.98600 69.41700 scale (grids/A): 1.538528 object centre (A): 14.32000 56.35600 31.16550 number of atom coordinates read : 4344 total number of charged atoms : 4139 net assigned charge : 3.306056 assigned positive charge : 653.0941 centred at (gu) : 91.81911 86.99109 82.56961 assigned negative charge : -649.7921 centred at (gu) : 92.20998 86.99639 82.91441 start vw surface at 0.1800000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 80607 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39428 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 22897 mr = 54133 m= 2001 mr = 14861 m= 36 mr = 836 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 54 time to turn everything in is 0.5900000 number of dielectric boundary points 35711 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 520 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.7200000 number of grid points assigned charge 31188 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) : 0.5128427 object centre at (A) : 14.32000 56.35600 31.16550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.5073674E-03 -1.1365796E-02 midg,1,midg; midg,igrid,midg -2.9267822E-03 -7.3914644E-03 1,midg,midg; igrid,midg,midg 8.6809034E-03 -3.4413752E-03 gauss-seidel spectral radius is 0.9980900 estimated iterations to convergence 182 setup time was (sec) 0.9100000 now iterating at: 17:07:49 rms-change max change #iterations 3.629505 149.7943 at 10iterations 1.474138 48.92380 at 20iterations 0.5999330 21.76748 at 30iterations 0.2458857 8.287369 at 40iterations 9.9965841E-02 3.481493 at 50iterations 4.0825155E-02 1.438475 at 60iterations 1.6745636E-02 0.5521240 at 70iterations 6.9331205E-03 0.2666283 at 80iterations 2.9488697E-03 0.1063118 at 90iterations 1.3718675E-03 4.6280861E-02 at 100iterations 7.5979909E-04 2.8608322E-02 at 110iterations 5.0495029E-04 1.6910553E-02 at 120iterations finished qdiffx linear iterations at : 17:07:55 total time elapsed so far: 7.650000 # loops : 120 mean,max change (kT/e) : 5.0495029E-04 1.6910553E-02 energy calculations done at 7.650000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.820000 DelPhi exited at 17:07:56 7.821u 0.266s 0:08.44 95.7% 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 17:07:56 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: 349 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4344 !!! WARNING: GLM 182 has a net charge of -0.0940 !!! WARNING: HEM 841 has a net charge of -3.4000 !!! WARNING: FE 2 has a net charge of 1.4000 !!! WARNING: FE 3 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= 0.1200000 grid size : 179 scale,in grids/A, set to be: 2.307792 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): -13.17200 41.81200 ymin,ymax (A): 24.36300 88.34900 zmin,zma (A): -3.543000 65.87400 x,y,z range (A): 54.98400 63.98600 69.41700 scale (grids/A): 2.307792 object centre (A): 14.32000 56.35600 31.16550 number of atom coordinates read : 4344 total number of charged atoms : 4139 net assigned charge : 3.306056 assigned positive charge : 653.0941 centred at (gu) : 92.72827 85.48630 78.85389 assigned negative charge : -649.7921 centred at (gu) : 93.31493 85.49448 79.37151 start vw surface at 0.1900000 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 187836 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39428 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 82578 mr = 133505 m= 20569 mr = 63483 m= 2693 mr = 14533 m= 121 mr = 1539 m= 0 mr = 24 time to grow re-entrant surface = 0.8000000 no. cavity mid-points inaccessible to solvent = 203 time to turn everything in is 1.410000 number of dielectric boundary points 80713 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 58 iepsmp to db, and charging done at 1.550000 number of grid points assigned charge 33023 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) : 1.538528 object centre at (A) : 14.32000 56.35600 31.16550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1329324 -0.2378283 midg,1,midg; midg,igrid,midg -0.1207187 -0.2508317 1,midg,midg; igrid,midg,midg 0.1023427 -4.0864442E-02 gauss-seidel spectral radius is 0.9991484 estimated iterations to convergence 271 setup time was (sec) 1.730000 now iterating at: 17:07:58 rms-change max change #iterations 9.881111 411.8801 at 10iterations 5.644502 158.7167 at 20iterations 3.194845 86.96626 at 30iterations 1.803101 40.38564 at 40iterations 1.014255 23.07090 at 50iterations 0.5662976 12.32146 at 60iterations 0.3165865 6.893850 at 70iterations 0.1765020 4.248991 at 80iterations 9.8465040E-02 2.087131 at 90iterations 5.4852299E-02 1.565515 at 100iterations 3.0461922E-02 0.6513786 at 110iterations 1.6920846E-02 0.3227177 at 120iterations 9.4362758E-03 0.1916475 at 130iterations 5.2776602E-03 0.1132541 at 140iterations 2.9915469E-03 6.4613342E-02 at 150iterations 1.7454217E-03 3.8070679E-02 at 160iterations 1.0732566E-03 2.3694992E-02 at 170iterations 7.0889445E-04 1.5565872E-02 at 180iterations finished qdiffx linear iterations at : 17:08:08 total time elapsed so far: 12.13000 # loops : 180 mean,max change (kT/e) : 7.0889445E-04 1.5565872E-02 energy calculations done at 12.13000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.31000 DelPhi exited at 17:08:09 12.311u 0.236s 0:12.84 97.6% 0+0k 0+0io 0pf+0w