Mon Oct 10 14:42:31 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 14:42:32 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: 309 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2423 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6079858 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): -5.372000 46.35100 ymin,ymax (A): -25.43900 33.11500 zmin,zma (A): 9.250000 64.20200 x,y,z range (A): 51.72300 58.55400 54.95200 scale (grids/A): 0.6079858 object centre (A): 20.48950 3.838001 36.72600 number of atom coordinates read : 2423 total number of charged atoms : 2278 net assigned charge : -1.999992 assigned positive charge : 358.6772 centred at (gu) : 88.48168 90.66027 89.38921 assigned negative charge : -360.6777 centred at (gu) : 88.33451 90.54668 89.35978 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 5962 nv = 96 ne = 84 npr = 48985 no. pairs analyzed = 48985 no. exposed pairs = 3233 no. arc points = 22878 no. surface atoms = 1096 nbur = 1327 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 269 mr = 3020 m= 0 mr = 12 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 3199 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2254 ## 261 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 7353 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.6238267E-09 2.1066546E-10 midg,1,midg; midg,igrid,midg -5.1517866E-09 4.4564792E-09 1,midg,midg; igrid,midg,midg -1.0580501E-08 3.6941863E-09 gauss-seidel spectral radius is 0.9859850 estimated iterations to convergence 69 setup time was (sec) 0.5700000 now iterating at: 14:42:33 rms-change max change #iterations 0.1106575 25.40582 at 10iterations 9.6036335E-03 1.650246 at 20iterations 8.4670639E-04 0.1333466 at 30iterations 7.4028212E-05 1.2878418E-02 at 40iterations 6.4524825E-06 9.8991394E-04 at 50iterations finished qdiffx linear iterations at : 14:42:36 total time elapsed so far: 4.330000 # loops : 50 mean,max change (kT/e) : 6.4524825E-06 9.8991394E-04 energy calculations done at 4.330000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.480000 DelPhi exited at 14:42:37 4.487u 0.387s 0:05.34 91.0% 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 14:42:37 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: 309 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2423 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.823957 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): -5.372000 46.35100 ymin,ymax (A): -25.43900 33.11500 zmin,zma (A): 9.250000 64.20200 x,y,z range (A): 51.72300 58.55400 54.95200 scale (grids/A): 1.823957 object centre (A): 20.48950 3.838001 36.72600 number of atom coordinates read : 2423 total number of charged atoms : 2278 net assigned charge : -1.999992 assigned positive charge : 358.6772 centred at (gu) : 85.44453 91.98038 88.16718 assigned negative charge : -360.6777 centred at (gu) : 85.00334 91.63990 88.07925 start vw surface at 0.1100000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 64486 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22878 grid for indexing accessible points = 1.400000 m= 21080 mr = 42972 m= 2701 mr = 14414 m= 103 mr = 1412 m= 0 mr = 15 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5400000 number of dielectric boundary points 29557 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 179 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 17817 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) : 0.6079858 object centre at (A) : 20.48950 3.838001 36.72600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.8220592E-02 1.3515139E-03 midg,1,midg; midg,igrid,midg -1.0593676E-03 3.4832321E-03 1,midg,midg; igrid,midg,midg -7.2730929E-03 7.9584261E-03 gauss-seidel spectral radius is 0.9984937 estimated iterations to convergence 204 setup time was (sec) 0.8200000 now iterating at: 14:42:38 rms-change max change #iterations 3.766060 204.4197 at 10iterations 1.686374 65.24565 at 20iterations 0.7610758 29.23299 at 30iterations 0.3423236 12.15986 at 40iterations 0.1543867 6.015956 at 50iterations 6.9351912E-02 2.437994 at 60iterations 3.1257160E-02 1.010529 at 70iterations 1.4054922E-02 0.4976349 at 80iterations 6.3433489E-03 0.2243156 at 90iterations 2.8493074E-03 9.7549438E-02 at 100iterations 1.2900175E-03 5.0964355E-02 at 110iterations 5.8166072E-04 2.0458221E-02 at 120iterations finished qdiffx linear iterations at : 14:42:48 total time elapsed so far: 10.77000 # loops : 120 mean,max change (kT/e) : 5.8166072E-04 2.0458221E-02 energy calculations done at 10.77000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.94000 DelPhi exited at 14:42:49 10.947u 0.447s 0:11.89 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 Mon Oct 10 2011 at 14:42:49 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: 309 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2423 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.735936 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): -5.372000 46.35100 ymin,ymax (A): -25.43900 33.11500 zmin,zma (A): 9.250000 64.20200 x,y,z range (A): 51.72300 58.55400 54.95200 scale (grids/A): 2.735936 object centre (A): 20.48950 3.838001 36.72600 number of atom coordinates read : 2423 total number of charged atoms : 2278 net assigned charge : -1.999992 assigned positive charge : 358.6772 centred at (gu) : 83.16670 92.97053 87.25073 assigned negative charge : -360.6777 centred at (gu) : 82.50508 92.45988 87.11887 start vw surface at 0.1100000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 149165 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22878 grid for indexing accessible points = 1.400000 m= 69826 mr = 104531 m= 22760 mr = 55032 m= 4527 mr = 17279 m= 496 mr = 2954 m= 18 mr = 237 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.8000001 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.360000 number of dielectric boundary points 66760 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.480000 number of grid points assigned charge 18218 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) : 1.823957 object centre at (A) : 20.48950 3.838001 36.72600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.6916962 0.1366382 midg,1,midg; midg,igrid,midg 2.4035344E-02 7.5248010E-02 1,midg,midg; igrid,midg,midg -3.4718454E-02 7.5754680E-02 gauss-seidel spectral radius is 0.9992182 estimated iterations to convergence 282 setup time was (sec) 1.670000 now iterating at: 14:42:51 rms-change max change #iterations 8.992105 322.8387 at 10iterations 5.175592 112.8906 at 20iterations 2.951858 76.93274 at 30iterations 1.686322 36.20882 at 40iterations 0.9591020 21.84470 at 50iterations 0.5446982 11.63770 at 60iterations 0.3091821 6.453186 at 70iterations 0.1750692 3.504984 at 80iterations 9.9295251E-02 2.033541 at 90iterations 5.5979680E-02 1.321251 at 100iterations 3.1794179E-02 0.6348715 at 110iterations 1.7966120E-02 0.3659687 at 120iterations 1.0159379E-02 0.2114124 at 130iterations 5.7465252E-03 0.1124420 at 140iterations 3.2567044E-03 7.1135283E-02 at 150iterations 1.8332079E-03 3.6615133E-02 at 160iterations 1.0372748E-03 2.0887375E-02 at 170iterations 5.8712834E-04 1.1398315E-02 at 180iterations finished qdiffx linear iterations at : 14:43:07 total time elapsed so far: 17.46000 # loops : 180 mean,max change (kT/e) : 5.8712834E-04 1.1398315E-02 energy calculations done at 17.46000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.63000 DelPhi exited at 14:43:08 17.631u 0.466s 0:18.59 97.3% 0+0k 0+0io 0pf+0w