Sat Oct 8 11:38:17 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 Sat Oct 8 2011 at 11:38:17 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: 242 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3157 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.6171342 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): 3.700000 61.33600 ymin,ymax (A): -8.701000 38.68700 zmin,zma (A): -19.32600 38.36000 x,y,z range (A): 57.63600 47.38800 57.68600 scale (grids/A): 0.6171342 object centre (A): 32.51800 14.99300 9.516998 number of atom coordinates read : 3157 total number of charged atoms : 3004 net assigned charge : -9.999962 assigned positive charge : 458.9876 centred at (gu) : 89.40600 90.51157 91.06156 assigned negative charge : -468.9887 centred at (gu) : 89.23946 90.58866 91.16936 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 8095 nv = 96 ne = 84 npr = 66101 no. pairs analyzed = 66101 no. exposed pairs = 3762 no. arc points = 25261 no. surface atoms = 1304 nbur = 1853 mkacc time = 0.1600000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 410 mr = 4674 m= 4 mr = 51 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 30 time to turn everything in is 0.3600000 number of dielectric boundary points 3784 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2484 ## 182 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 9914 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.9481219E-10 -1.9200534E-08 midg,1,midg; midg,igrid,midg -1.3756429E-09 -1.4397193E-08 1,midg,midg; igrid,midg,midg -2.2417577E-08 4.2594199E-09 gauss-seidel spectral radius is 0.9864499 estimated iterations to convergence 70 setup time was (sec) 0.6000000 now iterating at: 11:38:18 rms-change max change #iterations 0.1395177 19.46763 at 10iterations 1.3818196E-02 2.000519 at 20iterations 1.8963794E-03 0.2666454 at 30iterations 5.9420703E-04 8.4770203E-02 at 40iterations 2.4508164E-04 3.4803391E-02 at 50iterations finished qdiffx linear iterations at : 11:38:21 total time elapsed so far: 3.200000 # loops : 50 mean,max change (kT/e) : 2.4508164E-04 3.4803391E-02 energy calculations done at 3.200000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.390000 DelPhi exited at 11:38:21 3.393u 0.162s 0:04.06 87.4% 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 Sat Oct 8 2011 at 11:38:22 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: 242 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3157 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: 1.851403 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): 3.700000 61.33600 ymin,ymax (A): -8.701000 38.68700 zmin,zma (A): -19.32600 38.36000 x,y,z range (A): 57.63600 47.38800 57.68600 scale (grids/A): 1.851403 object centre (A): 32.51800 14.99300 9.516998 number of atom coordinates read : 3157 total number of charged atoms : 3004 net assigned charge : -9.999962 assigned positive charge : 458.9876 centred at (gu) : 88.21745 91.53348 93.18400 assigned negative charge : -468.9887 centred at (gu) : 87.71751 91.76557 93.50775 start vw surface at 0.1600000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 88994 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25261 grid for indexing accessible points = 1.400000 m= 32480 mr = 64389 m= 4951 mr = 23998 m= 246 mr = 3022 m= 2 mr = 70 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 952 time to turn everything in is 0.6400000 number of dielectric boundary points 35194 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 156 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 23615 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) : 0.6171342 object centre at (A) : 32.51800 14.99300 9.516998 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.6962904E-02 -5.0564066E-02 midg,1,midg; midg,igrid,midg -2.1798264E-02 -3.3670515E-02 1,midg,midg; igrid,midg,midg -3.1462390E-02 5.0057702E-02 gauss-seidel spectral radius is 0.9986084 estimated iterations to convergence 212 setup time was (sec) 0.9300000 now iterating at: 11:38:23 rms-change max change #iterations 4.449656 190.1447 at 10iterations 2.071725 60.81009 at 20iterations 0.9678879 30.05057 at 30iterations 0.4511301 14.86414 at 40iterations 0.2102167 6.453979 at 50iterations 9.8128766E-02 2.807327 at 60iterations 4.5991257E-02 1.418383 at 70iterations 2.1565577E-02 0.6236014 at 80iterations 1.0203167E-02 0.3620148 at 90iterations 4.9439892E-03 0.1542740 at 100iterations 2.5098033E-03 7.8639984E-02 at 110iterations 1.3693101E-03 4.4679642E-02 at 120iterations finished qdiffx linear iterations at : 11:38:29 total time elapsed so far: 7.400000 # loops : 120 mean,max change (kT/e) : 1.3693101E-03 4.4679642E-02 energy calculations done at 7.400000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.580000 DelPhi exited at 11:38:30 7.581u 0.171s 0:08.68 89.2% 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 11:38:30 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: 242 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3157 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: 2.777104 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): 3.700000 61.33600 ymin,ymax (A): -8.701000 38.68700 zmin,zma (A): -19.32600 38.36000 x,y,z range (A): 57.63600 47.38800 57.68600 scale (grids/A): 2.777104 object centre (A): 32.51800 14.99300 9.516998 number of atom coordinates read : 3157 total number of charged atoms : 3004 net assigned charge : -9.999962 assigned positive charge : 458.9876 centred at (gu) : 87.32597 92.29999 94.77594 assigned negative charge : -468.9887 centred at (gu) : 86.57616 92.64816 95.26155 start vw surface at 0.1600000 fill in re-entrant regions at 0.5200000 boundary points on vw surface= 206248 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25261 grid for indexing accessible points = 1.400000 m= 106895 mr = 155821 m= 37425 mr = 88219 m= 8895 mr = 29880 m= 1093 mr = 6530 m= 27 mr = 652 m= 0 mr = 0 time to grow re-entrant surface = 1.000000 no. cavity mid-points inaccessible to solvent = 3154 time to turn everything in is 1.640000 number of dielectric boundary points 79481 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.780000 number of grid points assigned charge 24031 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) : 1.851403 object centre at (A) : 32.51800 14.99300 9.516998 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.4856861 -0.5366013 midg,1,midg; midg,igrid,midg -0.3064011 -0.3374106 1,midg,midg; igrid,midg,midg -0.3732725 0.7368757 gauss-seidel spectral radius is 0.9992672 estimated iterations to convergence 292 setup time was (sec) 1.940000 now iterating at: 11:38:34 rms-change max change #iterations 10.63989 335.9935 at 10iterations 6.292037 139.8185 at 20iterations 3.684585 69.90125 at 30iterations 2.153682 44.68604 at 40iterations 1.253314 22.59254 at 50iterations 0.7281606 12.56139 at 60iterations 0.4223132 7.968748 at 70iterations 0.2443310 4.204584 at 80iterations 0.1419248 2.409842 at 90iterations 8.2234517E-02 1.423881 at 100iterations 4.7629647E-02 0.8043022 at 110iterations 2.7716568E-02 0.5052414 at 120iterations 1.6210960E-02 0.2749386 at 130iterations 9.6064918E-03 0.1705704 at 140iterations 5.8158655E-03 0.1063404 at 150iterations 3.6547421E-03 6.9656372E-02 at 160iterations 2.4249435E-03 4.5799255E-02 at 170iterations 1.7179162E-03 3.2127380E-02 at 180iterations finished qdiffx linear iterations at : 11:38:55 total time elapsed so far: 12.39000 # loops : 180 mean,max change (kT/e) : 1.7179162E-03 3.2127380E-02 energy calculations done at 12.39000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.59000 DelPhi exited at 11:38:56 12.592u 0.201s 0:26.03 49.1% 0+0k 0+0io 0pf+0w