Sat Oct 8 17:25:38 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 Sat Oct 8 2011 at 17:25:38 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3381 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5390428 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): -14.09700 43.10000 ymin,ymax (A): -38.36000 27.68300 zmin,zma (A): -15.77700 33.90400 x,y,z range (A): 57.19700 66.04300 49.68100 scale (grids/A): 0.5390428 object centre (A): 14.50150 -5.338500 9.063501 number of atom coordinates read : 3381 total number of charged atoms : 3235 net assigned charge : -1.999990 assigned positive charge : 506.5215 centred at (gu) : 90.44581 91.51435 90.45187 assigned negative charge : -508.5228 centred at (gu) : 90.47176 91.47156 90.41629 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 6179 nv = 96 ne = 84 npr = 69584 no. pairs analyzed = 69584 no. exposed pairs = 4046 no. arc points = 27995 no. surface atoms = 1379 nbur = 2002 mkacc time = 0.2000000 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 = 1.596000 m= 224 mr = 3344 m= 2 mr = 3 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4200000 number of dielectric boundary points 3058 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2805 ## 395 charges are in solution ## iepsmp to db, and charging done at 0.5400000 number of grid points assigned charge 8188 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.7431371E-10 1.2145587E-10 midg,1,midg; midg,igrid,midg -2.3968033E-10 2.2288732E-10 1,midg,midg; igrid,midg,midg 4.5968555E-11 -2.8025132E-10 gauss-seidel spectral radius is 0.9822837 estimated iterations to convergence 62 setup time was (sec) 0.6900000 now iterating at: 17:25:39 rms-change max change #iterations 7.5356223E-02 12.98603 at 10iterations 4.8792679E-03 0.7461166 at 20iterations 3.6424294E-04 5.9267163E-02 at 30iterations 4.7703517E-05 1.0474205E-02 at 40iterations 1.1009514E-05 2.2764206E-03 at 50iterations finished qdiffx linear iterations at : 17:25:42 total time elapsed so far: 3.990000 # loops : 50 mean,max change (kT/e) : 1.1009514E-05 2.2764206E-03 energy calculations done at 3.990000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.160000 DelPhi exited at 17:25:43 4.162u 0.262s 0:04.69 94.2% 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 Sat Oct 8 2011 at 17:25:43 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3381 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.617128 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): -14.09700 43.10000 ymin,ymax (A): -38.36000 27.68300 zmin,zma (A): -15.77700 33.90400 x,y,z range (A): 57.19700 66.04300 49.68100 scale (grids/A): 1.617128 object centre (A): 14.50150 -5.338500 9.063501 number of atom coordinates read : 3381 total number of charged atoms : 3235 net assigned charge : -1.999990 assigned positive charge : 506.5215 centred at (gu) : 91.33672 94.54195 91.35500 assigned negative charge : -508.5228 centred at (gu) : 91.41507 94.41423 91.24859 start vw surface at 0.1700000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 68781 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27995 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 21061 mr = 47603 m= 2128 mr = 14649 m= 49 mr = 1026 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 566 time to turn everything in is 0.6200000 number of dielectric boundary points 28741 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 338 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 24672 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) : 0.5390428 object centre at (A) : 14.50150 -5.338500 9.063501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.0167452E-03 4.1709035E-03 midg,1,midg; midg,igrid,midg 4.7895652E-03 4.8337835E-03 1,midg,midg; igrid,midg,midg -3.6197687E-03 -1.2012427E-02 gauss-seidel spectral radius is 0.9981776 estimated iterations to convergence 186 setup time was (sec) 0.9200000 now iterating at: 17:25:44 rms-change max change #iterations 3.465380 166.2406 at 10iterations 1.447580 47.03371 at 20iterations 0.6031142 22.74211 at 30iterations 0.2507062 8.611443 at 40iterations 0.1043894 3.763088 at 50iterations 4.3631580E-02 1.452586 at 60iterations 1.8228181E-02 0.6232491 at 70iterations 7.5910408E-03 0.3164520 at 80iterations 3.1802582E-03 0.1227937 at 90iterations 1.3278167E-03 4.5367241E-02 at 100iterations 5.5635039E-04 1.9608259E-02 at 110iterations 2.3447233E-04 9.3245506E-03 at 120iterations finished qdiffx linear iterations at : 17:25:52 total time elapsed so far: 9.130000 # loops : 120 mean,max change (kT/e) : 2.3447233E-04 9.3245506E-03 energy calculations done at 9.130000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.310000 DelPhi exited at 17:25:53 9.311u 0.295s 0:09.86 97.3% 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 Sat Oct 8 2011 at 17:25:53 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3381 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.425692 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): -14.09700 43.10000 ymin,ymax (A): -38.36000 27.68300 zmin,zma (A): -15.77700 33.90400 x,y,z range (A): 57.19700 66.04300 49.68100 scale (grids/A): 2.425692 object centre (A): 14.50150 -5.338500 9.063501 number of atom coordinates read : 3381 total number of charged atoms : 3235 net assigned charge : -1.999990 assigned positive charge : 506.5215 centred at (gu) : 92.00465 96.81277 92.03249 assigned negative charge : -508.5228 centred at (gu) : 92.12249 96.62121 91.87261 start vw surface at 0.1800000 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 159928 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27995 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 73778 mr = 116326 m= 20658 mr = 58731 m= 3355 mr = 15628 m= 210 mr = 2187 m= 2 mr = 82 m= 0 mr = 0 time to grow re-entrant surface = 0.9000000 no. cavity mid-points inaccessible to solvent = 1924 time to turn everything in is 1.540000 number of dielectric boundary points 64977 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 23 iepsmp to db, and charging done at 1.700000 number of grid points assigned charge 25848 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) : 1.617128 object centre at (A) : 14.50150 -5.338500 9.063501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1046261 6.4731799E-02 midg,1,midg; midg,igrid,midg 0.1182381 0.1940494 1,midg,midg; igrid,midg,midg -8.0696113E-02 -0.1615052 gauss-seidel spectral radius is 0.9991369 estimated iterations to convergence 269 setup time was (sec) 1.860000 now iterating at: 17:25:55 rms-change max change #iterations 9.038706 252.5607 at 10iterations 5.092588 112.1926 at 20iterations 2.840954 58.25618 at 30iterations 1.578628 33.28470 at 40iterations 0.8771787 18.78072 at 50iterations 0.4845338 10.02967 at 60iterations 0.2679023 5.862091 at 70iterations 0.1476005 3.125990 at 80iterations 8.1483886E-02 1.932640 at 90iterations 4.4861905E-02 0.8709621 at 100iterations 2.4707297E-02 0.5264854 at 110iterations 1.3599248E-02 0.3034191 at 120iterations 7.4797701E-03 0.1419106 at 130iterations 4.1233334E-03 7.7333450E-02 at 140iterations 2.2697831E-03 4.9986839E-02 at 150iterations 1.2538703E-03 2.6260376E-02 at 160iterations 6.9616956E-04 1.2812614E-02 at 170iterations 3.8893463E-04 8.3236694E-03 at 180iterations finished qdiffx linear iterations at : 17:26:08 total time elapsed so far: 15.30000 # loops : 180 mean,max change (kT/e) : 3.8893463E-04 8.3236694E-03 energy calculations done at 15.30000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.47000 DelPhi exited at 17:26:09 15.472u 0.305s 0:16.04 98.3% 0+0k 0+0io 0pf+0w