Sun Oct 9 03:49:36 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 Sun Oct 9 2011 at 03:49:36 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: 361 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4945 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.4335753 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): -12.01700 56.10200 ymin,ymax (A): -11.40000 47.29500 zmin,zma (A): 16.13100 98.23900 x,y,z range (A): 68.11900 58.69500 82.10800 scale (grids/A): 0.4335753 object centre (A): 22.04250 17.94750 57.18500 number of atom coordinates read : 4945 total number of charged atoms : 4706 net assigned charge : 14.50001 assigned positive charge : 735.8458 centred at (gu) : 91.28807 90.96761 93.29214 assigned negative charge : -721.3521 centred at (gu) : 91.36095 91.00002 93.36271 start vw surface at 0.1200000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 5591 nv = 96 ne = 84 npr = 99484 no. pairs analyzed = 99484 no. exposed pairs = 6308 no. arc points = 44295 no. surface atoms = 2103 nbur = 2842 mkacc time = 0.1700000 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 = 1.932000 m= 145 mr = 2665 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3100000 number of dielectric boundary points 3071 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3635 ## 804 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 7623 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.7930160E-12 -4.0489628E-13 midg,1,midg; midg,igrid,midg 4.1030200E-12 2.7265319E-12 1,midg,midg; igrid,midg,midg 5.1473882E-12 -2.7108545E-13 gauss-seidel spectral radius is 0.9728941 estimated iterations to convergence 51 setup time was (sec) 0.5000000 now iterating at: 03:49:37 rms-change max change #iterations 2.9774660E-02 5.226782 at 10iterations 2.5891720E-03 0.4663315 at 20iterations 5.7182508E-04 9.1636658E-02 at 30iterations 1.3558965E-04 2.0656586E-02 at 40iterations 3.2434873E-05 4.8217773E-03 at 50iterations finished qdiffx linear iterations at : 03:49:40 total time elapsed so far: 3.530000 # loops : 50 mean,max change (kT/e) : 3.2434873E-05 4.8217773E-03 energy calculations done at 3.530000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.670000 DelPhi exited at 03:49:40 3.671u 0.197s 0:04.20 91.9% 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 Sun Oct 9 2011 at 03:49:40 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: 361 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4945 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.300726 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): -12.01700 56.10200 ymin,ymax (A): -11.40000 47.29500 zmin,zma (A): 16.13100 98.23900 x,y,z range (A): 68.11900 58.69500 82.10800 scale (grids/A): 1.300726 object centre (A): 22.04250 17.94750 57.18500 number of atom coordinates read : 4945 total number of charged atoms : 4706 net assigned charge : 14.50001 assigned positive charge : 735.8458 centred at (gu) : 93.86287 92.90096 99.87446 assigned negative charge : -721.3521 centred at (gu) : 94.08270 93.00004 100.0883 start vw surface at 0.1300000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 65477 reading accessible surface arcs data from file ARCDAT no. of arc points read = 44295 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.820000 m= 14676 mr = 43195 m= 739 mr = 8654 m= 5 mr = 148 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 947 time to turn everything in is 0.3500000 number of dielectric boundary points 28900 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 829 ## 22 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 32840 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) : 0.4335753 object centre at (A) : 22.04250 17.94750 57.18500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.2298414E-03 -7.9426114E-03 midg,1,midg; midg,igrid,midg 1.7325599E-03 2.3915845E-03 1,midg,midg; igrid,midg,midg 6.2023499E-03 3.7330510E-03 gauss-seidel spectral radius is 0.9972736 estimated iterations to convergence 153 setup time was (sec) 0.5600000 now iterating at: 03:49:41 rms-change max change #iterations 2.551409 117.0460 at 10iterations 0.8686572 39.56208 at 20iterations 0.2976633 12.99656 at 30iterations 0.1027168 4.038674 at 40iterations 3.5628937E-02 1.320583 at 50iterations 1.2525667E-02 0.5109618 at 60iterations 4.6510687E-03 0.1825905 at 70iterations 1.9029179E-03 8.0760956E-02 at 80iterations 9.0006436E-04 3.5987854E-02 at 90iterations 4.8344524E-04 1.7616272E-02 at 100iterations 2.7975591E-04 9.8838806E-03 at 110iterations 1.6626454E-04 5.6838989E-03 at 120iterations finished qdiffx linear iterations at : 03:49:48 total time elapsed so far: 7.660000 # loops : 120 mean,max change (kT/e) : 1.6626454E-04 5.6838989E-03 energy calculations done at 7.660000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.800000 DelPhi exited at 03:49:49 7.802u 0.206s 0:08.27 96.7% 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 Sun Oct 9 2011 at 03:49:49 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: 361 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4945 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.951089 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): -12.01700 56.10200 ymin,ymax (A): -11.40000 47.29500 zmin,zma (A): 16.13100 98.23900 x,y,z range (A): 68.11900 58.69500 82.10800 scale (grids/A): 1.951089 object centre (A): 22.04250 17.94750 57.18500 number of atom coordinates read : 4945 total number of charged atoms : 4706 net assigned charge : 14.50001 assigned positive charge : 735.8458 centred at (gu) : 95.79365 94.35135 104.8115 assigned negative charge : -721.3521 centred at (gu) : 96.12400 94.49998 105.1322 start vw surface at 0.1400000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 154125 reading accessible surface arcs data from file ARCDAT no. of arc points read = 44295 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.792000 m= 57955 mr = 108356 m= 9651 mr = 42715 m= 651 mr = 5952 m= 13 mr = 253 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.4100000 no. cavity mid-points inaccessible to solvent = 3140 time to turn everything in is 0.7900000 number of dielectric boundary points 65120 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 238 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.8900000 number of grid points assigned charge 37081 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) : 1.300726 object centre at (A) : 22.04250 17.94750 57.18500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.0220909E-02 -0.2670505 midg,1,midg; midg,igrid,midg 4.0668357E-02 7.3404759E-02 1,midg,midg; igrid,midg,midg 0.1747855 9.9956870E-02 gauss-seidel spectral radius is 0.9988810 estimated iterations to convergence 237 setup time was (sec) 1.040000 now iterating at: 03:49:50 rms-change max change #iterations 7.761132 272.7032 at 10iterations 4.046382 118.9686 at 20iterations 2.094006 55.57775 at 30iterations 1.080033 28.52923 at 40iterations 0.5548829 14.18746 at 50iterations 0.2833228 6.270077 at 60iterations 0.1445611 3.570099 at 70iterations 7.3674329E-02 2.003675 at 80iterations 3.7382137E-02 0.9362144 at 90iterations 1.9085025E-02 0.4209862 at 100iterations 9.7183110E-03 0.2248917 at 110iterations 4.9420460E-03 0.1226190 at 120iterations 2.5375241E-03 5.9226990E-02 at 130iterations 1.3075735E-03 3.4328461E-02 at 140iterations 6.8687566E-04 1.6529083E-02 at 150iterations 3.6937778E-04 9.2636421E-03 at 160iterations 2.0578734E-04 5.1956177E-03 at 170iterations 1.2007287E-04 2.7465820E-03 at 180iterations finished qdiffx linear iterations at : 03:50:01 total time elapsed so far: 12.49000 # loops : 180 mean,max change (kT/e) : 1.2007287E-04 2.7465820E-03 energy calculations done at 12.49000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.62000 DelPhi exited at 03:50:02 12.623u 0.222s 0:13.11 97.9% 0+0k 0+0io 0pf+0w