Mon Oct 10 17:01:27 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 17:01:27 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: 292 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2636 !!! WARNING: GLM 155 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5373666 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): -8.487000 38.45600 ymin,ymax (A): -9.213000 42.37200 zmin,zma (A): -1.449000 64.80000 x,y,z range (A): 46.94300 51.58500 66.24900 scale (grids/A): 0.5373666 object centre (A): 14.98450 16.57950 31.67550 number of atom coordinates read : 2636 total number of charged atoms : 2491 net assigned charge : -9.3973517E-02 assigned positive charge : 389.7238 centred at (gu) : 90.43980 89.09192 88.90752 assigned negative charge : -389.8187 centred at (gu) : 90.39088 89.00839 89.00287 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 5011 nv = 96 ne = 84 npr = 53055 no. pairs analyzed = 53055 no. exposed pairs = 3434 no. arc points = 24055 no. surface atoms = 1152 nbur = 1484 mkacc time = 9.0000004E-02 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= 173 mr = 2518 m= 0 mr = 6 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2000000 number of dielectric boundary points 2660 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2492 ## 360 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 6567 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.1499138E-10 -3.1127478E-10 midg,1,midg; midg,igrid,midg -4.5465010E-10 2.7022914E-10 1,midg,midg; igrid,midg,midg -1.8998390E-10 2.2135288E-10 gauss-seidel spectral radius is 0.9821291 estimated iterations to convergence 62 setup time was (sec) 0.4300000 now iterating at: 17:01:27 rms-change max change #iterations 6.4887062E-02 12.46103 at 10iterations 4.1155703E-03 0.7937226 at 20iterations 2.5844193E-04 4.5617104E-02 at 30iterations 1.6822911E-05 2.7632713E-03 at 40iterations 1.1144022E-06 1.7166138E-04 at 50iterations finished qdiffx linear iterations at : 17:01:31 total time elapsed so far: 3.740000 # loops : 50 mean,max change (kT/e) : 1.1144022E-06 1.7166138E-04 energy calculations done at 3.740000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.870000 DelPhi exited at 17:01:32 3.873u 0.248s 0:04.84 84.9% 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 Mon Oct 10 2011 at 17:01:32 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: 292 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2636 !!! WARNING: GLM 155 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.612100 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): -8.487000 38.45600 ymin,ymax (A): -9.213000 42.37200 zmin,zma (A): -1.449000 64.80000 x,y,z range (A): 46.94300 51.58500 66.24900 scale (grids/A): 1.612100 object centre (A): 14.98450 16.57950 31.67550 number of atom coordinates read : 2636 total number of charged atoms : 2491 net assigned charge : -9.3973517E-02 assigned positive charge : 389.7238 centred at (gu) : 91.31909 87.27516 86.72182 assigned negative charge : -389.8187 centred at (gu) : 91.17251 87.02516 87.00842 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 55274 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24055 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 16637 mr = 36762 m= 1689 mr = 11298 m= 40 mr = 799 m= 0 mr = 2 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 149 time to turn everything in is 0.2900000 number of dielectric boundary points 24779 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 340 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 19080 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) : 0.5373666 object centre at (A) : 14.98450 16.57950 31.67550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.2639798E-02 -9.5486827E-03 midg,1,midg; midg,igrid,midg -9.0340683E-03 5.4456817E-04 1,midg,midg; igrid,midg,midg -1.8993634E-03 -9.0457697E-04 gauss-seidel spectral radius is 0.9980978 estimated iterations to convergence 182 setup time was (sec) 0.5600000 now iterating at: 17:01:33 rms-change max change #iterations 3.000099 158.1480 at 10iterations 1.220215 53.42069 at 20iterations 0.4975647 21.69960 at 30iterations 0.2027767 8.931087 at 40iterations 8.2987309E-02 3.649979 at 50iterations 3.3912167E-02 1.395366 at 60iterations 1.3821012E-02 0.5946617 at 70iterations 5.6407475E-03 0.2064800 at 80iterations 2.3061719E-03 0.1063118 at 90iterations 9.3834382E-04 3.9360046E-02 at 100iterations 3.8481798E-04 1.5792847E-02 at 110iterations 1.5667071E-04 6.2274933E-03 at 120iterations finished qdiffx linear iterations at : 17:01:40 total time elapsed so far: 8.380000 # loops : 120 mean,max change (kT/e) : 1.5667071E-04 6.2274933E-03 energy calculations done at 8.380000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.510000 DelPhi exited at 17:01:43 8.512u 0.284s 0:11.12 79.0% 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 17:01:43 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: 292 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2636 !!! WARNING: GLM 155 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.418150 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): -8.487000 38.45600 ymin,ymax (A): -9.213000 42.37200 zmin,zma (A): -1.449000 64.80000 x,y,z range (A): 46.94300 51.58500 66.24900 scale (grids/A): 2.418150 object centre (A): 14.98450 16.57950 31.67550 number of atom coordinates read : 2636 total number of charged atoms : 2491 net assigned charge : -9.3973517E-02 assigned positive charge : 389.7238 centred at (gu) : 91.97857 85.91266 85.08260 assigned negative charge : -389.8187 centred at (gu) : 91.75877 85.53755 85.51260 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 128311 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24055 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 58163 mr = 90115 m= 16123 mr = 45569 m= 2548 mr = 12000 m= 146 mr = 1629 m= 1 mr = 53 m= 0 mr = 0 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 545 time to turn everything in is 0.6800000 number of dielectric boundary points 55926 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 30 iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 19896 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) : 1.612100 object centre at (A) : 14.98450 16.57950 31.67550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1656747 -7.9946823E-02 midg,1,midg; midg,igrid,midg -0.1091627 1.5629297E-02 1,midg,midg; igrid,midg,midg -2.0504022E-02 -2.5895327E-02 gauss-seidel spectral radius is 0.9991029 estimated iterations to convergence 264 setup time was (sec) 0.9200000 now iterating at: 17:01:44 rms-change max change #iterations 7.817443 251.0704 at 10iterations 4.331827 122.3305 at 20iterations 2.372049 56.64536 at 30iterations 1.293904 29.60160 at 40iterations 0.7054828 16.62547 at 50iterations 0.3833176 9.414452 at 60iterations 0.2084878 4.951074 at 70iterations 0.1129617 2.587967 at 80iterations 6.1351605E-02 1.348930 at 90iterations 3.3305399E-02 0.7522736 at 100iterations 1.8013099E-02 0.3820760 at 110iterations 9.7609852E-03 0.2196102 at 120iterations 5.2795778E-03 0.1149445 at 130iterations 2.8663548E-03 6.1245918E-02 at 140iterations 1.5528258E-03 3.6052704E-02 at 150iterations 8.4046507E-04 1.8082619E-02 at 160iterations 4.5487462E-04 9.8800659E-03 at 170iterations 2.4646564E-04 5.3176880E-03 at 180iterations finished qdiffx linear iterations at : 17:01:56 total time elapsed so far: 12.60000 # loops : 180 mean,max change (kT/e) : 2.4646564E-04 5.3176880E-03 energy calculations done at 12.60000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.72000 DelPhi exited at 17:01:58 12.724u 0.228s 0:14.97 86.4% 0+0k 0+0io 0pf+0w