Sun Oct 9 20:41:48 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+sph.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 Sun Oct 9 2011 at 20:41:48 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4959 !!! WARNING: PLP 999 has a net charge of -0.3790 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: 0.5627213 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): 3.385000 64.47800 ymin,ymax (A): -7.836000 53.63800 zmin,zma (A): -1.144000 62.12000 x,y,z range (A): 61.09300 61.47400 63.26400 scale (grids/A): 0.5627213 object centre (A): 33.93150 22.90100 30.48800 number of atom coordinates read : 4959 total number of charged atoms : 4803 net assigned charge : 1.621042 assigned positive charge : 759.3810 centred at (gu) : 88.14833 89.05283 89.06256 assigned negative charge : -757.7655 centred at (gu) : 88.03812 89.05939 89.04177 start vw surface at 0.2000000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 10215 nv = 96 ne = 84 npr = 101596 no. pairs analyzed = 101596 no. exposed pairs = 5719 no. arc points = 38373 no. surface atoms = 1952 nbur = 3007 mkacc time = 0.2200000 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 = 1.512000 m= 475 mr = 5914 m= 2 mr = 35 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4600000 number of dielectric boundary points 4743 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3933 ## 409 charges are in solution ## iepsmp to db, and charging done at 0.5700000 number of grid points assigned charge 13379 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.4161703E-10 5.3421029E-10 midg,1,midg; midg,igrid,midg 4.7235460E-10 8.5346175E-11 1,midg,midg; igrid,midg,midg -3.2782170E-09 1.5910279E-09 gauss-seidel spectral radius is 0.9838522 estimated iterations to convergence 65 setup time was (sec) 0.7100000 now iterating at: 20:41:49 rms-change max change #iterations 0.1175367 16.29233 at 10iterations 1.1864141E-02 1.534866 at 20iterations 3.8102833E-03 0.4400444 at 30iterations 1.7868798E-03 0.2130194 at 40iterations 8.5516594E-04 0.1054735 at 50iterations finished qdiffx linear iterations at : 20:41:51 total time elapsed so far: 3.420000 # loops : 50 mean,max change (kT/e) : 8.5516594E-04 0.1054735 energy calculations done at 3.420000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.600000 DelPhi exited at 20:41:52 3.599u 0.226s 0:04.12 92.4% 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 Sun Oct 9 2011 at 20:41:52 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4959 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 1.688164 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): 3.385000 64.47800 ymin,ymax (A): -7.836000 53.63800 zmin,zma (A): -1.144000 62.12000 x,y,z range (A): 61.09300 61.47400 63.26400 scale (grids/A): 1.688164 object centre (A): 33.93150 22.90100 30.48800 number of atom coordinates read : 4959 total number of charged atoms : 4803 net assigned charge : 1.621042 assigned positive charge : 759.3810 centred at (gu) : 84.44344 87.15689 87.18636 assigned negative charge : -757.7655 centred at (gu) : 84.11409 87.17823 87.12517 start vw surface at 0.1900000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 113573 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38373 grid for indexing accessible points = 1.400000 m= 40764 mr = 82895 m= 5209 mr = 29922 m= 218 mr = 2965 m= 0 mr = 47 time to grow re-entrant surface = 0.3700000 no. cavity mid-points inaccessible to solvent = 185 time to turn everything in is 0.7500000 number of dielectric boundary points 43935 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 350 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.8800000 number of grid points assigned charge 37053 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) : 0.5627213 object centre at (A) : 33.93150 22.90100 30.48800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.9764466E-02 -2.9393701E-02 midg,1,midg; midg,igrid,midg 2.3503575E-02 1.4855018E-02 1,midg,midg; igrid,midg,midg -2.7796099E-02 4.1633513E-02 gauss-seidel spectral radius is 0.9984823 estimated iterations to convergence 204 setup time was (sec) 1.060000 now iterating at: 20:41:53 rms-change max change #iterations 4.926441 172.8446 at 10iterations 2.206294 72.71895 at 20iterations 0.9967483 26.32457 at 30iterations 0.4485410 11.82164 at 40iterations 0.2026380 5.679184 at 50iterations 9.1847472E-02 2.530087 at 60iterations 4.1795190E-02 1.150129 at 70iterations 1.9428400E-02 0.5315018 at 80iterations 9.5418673E-03 0.2706909 at 90iterations 5.1453989E-03 0.1583862 at 100iterations 3.1555698E-03 9.1241837E-02 at 110iterations 2.1723052E-03 6.3423157E-02 at 120iterations finished qdiffx linear iterations at : 20:42:00 total time elapsed so far: 7.760000 # loops : 120 mean,max change (kT/e) : 2.1723052E-03 6.3423157E-02 energy calculations done at 7.760000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.950000 DelPhi exited at 20:42:00 7.949u 0.269s 0:08.56 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 Sun Oct 9 2011 at 20:42:00 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4959 !!! WARNING: PLP 999 has a net charge of -0.3790 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: 2.532246 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): 3.385000 64.47800 ymin,ymax (A): -7.836000 53.63800 zmin,zma (A): -1.144000 62.12000 x,y,z range (A): 61.09300 61.47400 63.26400 scale (grids/A): 2.532246 object centre (A): 33.93150 22.90100 30.48800 number of atom coordinates read : 4959 total number of charged atoms : 4803 net assigned charge : 1.621042 assigned positive charge : 759.3810 centred at (gu) : 81.66492 85.73505 85.77917 assigned negative charge : -757.7655 centred at (gu) : 81.17126 85.76723 85.68775 start vw surface at 0.1900000 fill in re-entrant regions at 0.6000000 boundary points on vw surface= 263555 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38373 grid for indexing accessible points = 1.400000 m= 136004 mr = 200692 m= 44960 mr = 112196 m= 8828 mr = 35400 m= 844 mr = 6270 m= 16 mr = 456 m= 0 mr = 5 time to grow re-entrant surface = 1.190000 no. cavity mid-points inaccessible to solvent = 632 time to turn everything in is 1.950000 number of dielectric boundary points 99188 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 22 iepsmp to db, and charging done at 2.100000 number of grid points assigned charge 38400 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) : 1.688164 object centre at (A) : 33.93150 22.90100 30.48800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.5298247 -0.7331544 midg,1,midg; midg,igrid,midg 5.4610472E-02 8.6970396E-02 1,midg,midg; igrid,midg,midg -0.5176888 0.7534815 gauss-seidel spectral radius is 0.9992636 estimated iterations to convergence 291 setup time was (sec) 2.290000 now iterating at: 20:42:03 rms-change max change #iterations 12.34265 310.8480 at 10iterations 7.307430 155.8252 at 20iterations 4.292082 74.12975 at 30iterations 2.514302 44.03412 at 40iterations 1.471187 31.34251 at 50iterations 0.8562863 13.82073 at 60iterations 0.4968163 8.075424 at 70iterations 0.2883416 4.578220 at 80iterations 0.1672166 2.508788 at 90iterations 9.7057521E-02 1.621670 at 100iterations 5.6209777E-02 0.9936552 at 110iterations 3.2729965E-02 0.5258131 at 120iterations 1.9257355E-02 0.2846642 at 130iterations 1.1533858E-02 0.1892757 at 140iterations 7.1405475E-03 0.1142731 at 150iterations 4.6504852E-03 9.1171265E-02 at 160iterations 3.2573503E-03 5.8043480E-02 at 170iterations 2.4425238E-03 4.2533875E-02 at 180iterations finished qdiffx linear iterations at : 20:42:16 total time elapsed so far: 14.90000 # loops : 180 mean,max change (kT/e) : 2.4425238E-03 4.2533875E-02 energy calculations done at 14.90000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.08000 DelPhi exited at 20:42:16 15.077u 0.260s 0:15.63 98.0% 0+0k 0+0io 0pf+0w