Sun Oct 9 18:36:29 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 Sun Oct 9 2011 at 18:36:30 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: 313 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5248 !!! WARNING: HIQ 377 has a net charge of 0.5140 !!! 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= 0.1400000 grid size : 179 scale,in grids/A, set to be: 0.5377969 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): 3.330000 68.29300 ymin,ymax (A): -8.983000 56.81200 zmin,zma (A): -2.666000 63.53000 x,y,z range (A): 64.96300 65.79500 66.19600 scale (grids/A): 0.5377969 object centre (A): 35.81150 23.91450 30.43200 number of atom coordinates read : 5248 total number of charged atoms : 5114 net assigned charge : 3.635048 assigned positive charge : 811.3782 centred at (gu) : 88.20914 88.49713 89.48362 assigned negative charge : -807.7496 centred at (gu) : 88.08433 88.53658 89.42207 start vw surface at 0.2100000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 9905 nv = 96 ne = 84 npr = 105163 no. pairs analyzed = 105163 no. exposed pairs = 6200 no. arc points = 42499 no. surface atoms = 2119 nbur = 3129 mkacc time = 0.2900000 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= 429 mr = 5580 m= 1 mr = 26 m= 0 mr = 0 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5700000 number of dielectric boundary points 4729 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4282 ## 464 charges are in solution ## iepsmp to db, and charging done at 0.6900000 number of grid points assigned charge 13053 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.1472539E-10 6.3120098E-10 midg,1,midg; midg,igrid,midg 7.7208212E-10 -1.1130200E-10 1,midg,midg; igrid,midg,midg -1.4846995E-09 8.0485035E-10 gauss-seidel spectral radius is 0.9823442 estimated iterations to convergence 62 setup time was (sec) 0.8300000 now iterating at: 18:36:31 rms-change max change #iterations 9.6373521E-02 14.87534 at 10iterations 8.5003339E-03 1.180302 at 20iterations 2.3629600E-03 0.2731361 at 30iterations 1.0307168E-03 0.1170001 at 40iterations 4.6669412E-04 5.8231354E-02 at 50iterations finished qdiffx linear iterations at : 18:36:34 total time elapsed so far: 4.120000 # loops : 50 mean,max change (kT/e) : 4.6669412E-04 5.8231354E-02 energy calculations done at 4.120000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.290000 DelPhi exited at 18:36:34 4.298u 0.294s 0:04.85 94.4% 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 18:36:34 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: 313 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5248 !!! WARNING: HIQ 377 has a net charge of 0.5140 !!! 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= 0.1400000 grid size : 179 scale,in grids/A, set to be: 1.613391 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): 3.330000 68.29300 ymin,ymax (A): -8.983000 56.81200 zmin,zma (A): -2.666000 63.53000 x,y,z range (A): 64.96300 65.79500 66.19600 scale (grids/A): 1.613391 object centre (A): 35.81150 23.91450 30.43200 number of atom coordinates read : 5248 total number of charged atoms : 5114 net assigned charge : 3.635048 assigned positive charge : 811.3782 centred at (gu) : 84.62581 85.49019 88.44934 assigned negative charge : -807.7496 centred at (gu) : 84.25290 85.60966 88.26593 start vw surface at 0.2400000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 111327 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42499 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 37418 mr = 80291 m= 4112 mr = 26533 m= 111 mr = 2044 m= 1 mr = 2 m= 0 mr = 0 time to grow re-entrant surface = 0.5100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.9800000 number of dielectric boundary points 44099 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 476 ## 4 charges are in solution ## iepsmp to db, and charging done at 1.120000 number of grid points assigned charge 39038 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) : 0.5377969 object centre at (A) : 35.81150 23.91450 30.43200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.0010745E-02 -6.1456626E-03 midg,1,midg; midg,igrid,midg 2.4436336E-02 2.5940478E-02 1,midg,midg; igrid,midg,midg -5.3965524E-03 1.4190526E-02 gauss-seidel spectral radius is 0.9983485 estimated iterations to convergence 195 setup time was (sec) 1.280000 now iterating at: 18:36:36 rms-change max change #iterations 4.619912 158.8357 at 10iterations 2.005785 59.96443 at 20iterations 0.8723275 27.07166 at 30iterations 0.3792398 12.01126 at 40iterations 0.1654687 4.973503 at 50iterations 7.2625749E-02 1.986061 at 60iterations 3.2118767E-02 0.9089279 at 70iterations 1.4606267E-02 0.4303741 at 80iterations 7.1345204E-03 0.2045975 at 90iterations 3.9191479E-03 0.1109848 at 100iterations 2.4721478E-03 7.0158005E-02 at 110iterations 1.7218578E-03 4.6237946E-02 at 120iterations finished qdiffx linear iterations at : 18:36:44 total time elapsed so far: 9.800000 # loops : 120 mean,max change (kT/e) : 1.7218578E-03 4.6237946E-02 energy calculations done at 9.800000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.980000 DelPhi exited at 18:36:45 9.981u 0.290s 0:10.55 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 Sun Oct 9 2011 at 18:36:45 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: 313 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5248 !!! WARNING: HIQ 377 has a net charge of 0.5140 !!! 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= 0.1400000 grid size : 179 scale,in grids/A, set to be: 2.420086 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): 3.330000 68.29300 ymin,ymax (A): -8.983000 56.81200 zmin,zma (A): -2.666000 63.53000 x,y,z range (A): 64.96300 65.79500 66.19600 scale (grids/A): 2.420086 object centre (A): 35.81150 23.91450 30.43200 number of atom coordinates read : 5248 total number of charged atoms : 5114 net assigned charge : 3.635048 assigned positive charge : 811.3782 centred at (gu) : 81.93827 83.23483 87.67364 assigned negative charge : -807.7496 centred at (gu) : 81.37925 83.41431 87.39899 start vw surface at 0.2400000 fill in re-entrant regions at 0.7700000 boundary points on vw surface= 258623 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42499 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 128065 mr = 195408 m= 38704 mr = 103606 m= 6552 mr = 29577 m= 439 mr = 4245 m= 6 mr = 152 m= 0 mr = 0 time to grow re-entrant surface = 1.540000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.470000 number of dielectric boundary points 99401 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 26 iepsmp to db, and charging done at 2.630000 number of grid points assigned charge 40862 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) : 1.613391 object centre at (A) : 35.81150 23.91450 30.43200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2944517 -0.2219700 midg,1,midg; midg,igrid,midg 0.2223455 0.5883121 1,midg,midg; igrid,midg,midg -0.1399486 0.1682032 gauss-seidel spectral radius is 0.9992321 estimated iterations to convergence 285 setup time was (sec) 2.810000 now iterating at: 18:36:48 rms-change max change #iterations 11.94634 303.4585 at 10iterations 7.003606 133.8906 at 20iterations 4.071303 80.67103 at 30iterations 2.355910 53.79408 at 40iterations 1.358227 27.49486 at 50iterations 0.7801570 15.42388 at 60iterations 0.4484971 7.688668 at 70iterations 0.2566660 4.351232 at 80iterations 0.1468034 2.368281 at 90iterations 8.4291086E-02 1.450912 at 100iterations 4.8233081E-02 0.7489128 at 110iterations 2.7694780E-02 0.4489696 at 120iterations 1.6075483E-02 0.2909925 at 130iterations 9.4521185E-03 0.1772118 at 140iterations 5.7192007E-03 0.1033325 at 150iterations 3.6457749E-03 6.4380646E-02 at 160iterations 2.4892217E-03 4.4744492E-02 at 170iterations 1.8192939E-03 3.3639908E-02 at 180iterations finished qdiffx linear iterations at : 18:37:02 total time elapsed so far: 17.21000 # loops : 180 mean,max change (kT/e) : 1.8192939E-03 3.3639908E-02 energy calculations done at 17.22000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.40000 DelPhi exited at 18:37:03 17.398u 0.295s 0:17.96 98.4% 0+0k 0+0io 0pf+0w