Sat Oct 8 14:14:12 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 14:14:12 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2939 !!! WARNING: NAP 316 has a net charge of -2.0000 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: 0.6327764 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): -11.37200 43.41300 ymin,ymax (A): 10.43600 54.94600 zmin,zma (A): 36.26600 92.52600 x,y,z range (A): 54.78500 44.51000 56.26000 scale (grids/A): 0.6327764 object centre (A): 16.02050 32.69100 64.39600 number of atom coordinates read : 2939 total number of charged atoms : 2794 net assigned charge : -1.999992 assigned positive charge : 439.8817 centred at (gu) : 89.19238 89.58589 92.04942 assigned negative charge : -441.8825 centred at (gu) : 89.17719 89.50024 92.01511 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 7989 nv = 96 ne = 84 npr = 60640 no. pairs analyzed = 60640 no. exposed pairs = 3449 no. arc points = 23483 no. surface atoms = 1174 nbur = 1765 mkacc time = 0.1600000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 414 mr = 4710 m= 3 mr = 47 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3400000 number of dielectric boundary points 3649 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2283 ## 193 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 9601 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.9397818E-09 2.1923605E-09 midg,1,midg; midg,igrid,midg -1.2843834E-08 6.2107604E-09 1,midg,midg; igrid,midg,midg -4.7791122E-09 -6.2970806E-10 gauss-seidel spectral radius is 0.9870894 estimated iterations to convergence 72 setup time was (sec) 0.6600000 now iterating at: 14:14:13 rms-change max change #iterations 0.1531627 22.17284 at 10iterations 1.5325242E-02 2.367176 at 20iterations 1.5644162E-03 0.2137675 at 30iterations 2.0147148E-04 2.6268959E-02 at 40iterations 3.7215708E-05 5.9137344E-03 at 50iterations finished qdiffx linear iterations at : 14:14:17 total time elapsed so far: 4.430000 # loops : 50 mean,max change (kT/e) : 3.7215708E-05 5.9137344E-03 energy calculations done at 4.430000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.610000 DelPhi exited at 14:14:18 4.611u 0.386s 0:05.31 93.9% 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 Sat Oct 8 2011 at 14:14:18 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2939 !!! WARNING: NAP 316 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.898329 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): -11.37200 43.41300 ymin,ymax (A): 10.43600 54.94600 zmin,zma (A): 36.26600 92.52600 x,y,z range (A): 54.78500 44.51000 56.26000 scale (grids/A): 1.898329 object centre (A): 16.02050 32.69100 64.39600 number of atom coordinates read : 2939 total number of charged atoms : 2794 net assigned charge : -1.999992 assigned positive charge : 439.8817 centred at (gu) : 87.57638 88.75674 96.14752 assigned negative charge : -441.8825 centred at (gu) : 87.53145 88.50031 96.04502 start vw surface at 0.1300000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 87399 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23483 grid for indexing accessible points = 1.400000 m= 32958 mr = 63644 m= 5050 mr = 25141 m= 248 mr = 3155 m= 3 mr = 68 m= 0 mr = 0 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 138 time to turn everything in is 0.6900000 number of dielectric boundary points 33650 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 129 iepsmp to db, and charging done at 0.8100000 number of grid points assigned charge 21994 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) : 0.6327764 object centre at (A) : 16.02050 32.69100 64.39600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.4563278E-02 -1.5663533E-03 midg,1,midg; midg,igrid,midg -4.4983565E-03 1.1361258E-02 1,midg,midg; igrid,midg,midg -1.3775147E-02 7.4498081E-03 gauss-seidel spectral radius is 0.9986567 estimated iterations to convergence 216 setup time was (sec) 1.010000 now iterating at: 14:14:19 rms-change max change #iterations 4.577847 210.0744 at 10iterations 2.164133 66.63150 at 20iterations 1.023090 28.71054 at 30iterations 0.4811284 16.86870 at 40iterations 0.2273921 6.778904 at 50iterations 0.1072290 3.153628 at 60iterations 5.0577436E-02 1.465351 at 70iterations 2.3914421E-02 0.7064552 at 80iterations 1.1347921E-02 0.3547325 at 90iterations 5.3472840E-03 0.1642952 at 100iterations 2.5432766E-03 7.6786757E-02 at 110iterations 1.2019760E-03 3.7961960E-02 at 120iterations finished qdiffx linear iterations at : 14:14:30 total time elapsed so far: 11.76000 # loops : 120 mean,max change (kT/e) : 1.2019760E-03 3.7961960E-02 energy calculations done at 11.76000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.93000 DelPhi exited at 14:14:30 11.935u 0.458s 0:12.66 97.7% 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 Sat Oct 8 2011 at 14:14:30 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2939 !!! WARNING: NAP 316 has a net charge of -2.0000 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: 2.847494 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): -11.37200 43.41300 ymin,ymax (A): 10.43600 54.94600 zmin,zma (A): 36.26600 92.52600 x,y,z range (A): 54.78500 44.51000 56.26000 scale (grids/A): 2.847494 object centre (A): 16.02050 32.69100 64.39600 number of atom coordinates read : 2939 total number of charged atoms : 2794 net assigned charge : -1.999992 assigned positive charge : 439.8817 centred at (gu) : 86.36448 88.13499 99.22103 assigned negative charge : -441.8825 centred at (gu) : 86.29707 87.75043 99.06760 start vw surface at 0.1100000 fill in re-entrant regions at 0.6100000 boundary points on vw surface= 202523 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23483 grid for indexing accessible points = 1.400000 m= 107206 mr = 153533 m= 38911 mr = 90006 m= 8912 mr = 31870 m= 1152 mr = 6664 m= 36 mr = 771 m= 0 mr = 5 time to grow re-entrant surface = 1.140000 no. cavity mid-points inaccessible to solvent = 436 time to turn everything in is 1.880000 number of dielectric boundary points 75891 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 2.010000 number of grid points assigned charge 22346 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) : 1.898329 object centre at (A) : 16.02050 32.69100 64.39600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.8093562E-02 6.5841109E-02 midg,1,midg; midg,igrid,midg -3.1038376E-02 0.1425601 1,midg,midg; igrid,midg,midg 1.3278495E-02 0.2721023 gauss-seidel spectral radius is 0.9992685 estimated iterations to convergence 292 setup time was (sec) 2.210000 now iterating at: 14:14:33 rms-change max change #iterations 10.71761 402.7235 at 10iterations 6.306847 135.7891 at 20iterations 3.679830 74.18257 at 30iterations 2.146122 37.52064 at 40iterations 1.248495 22.90341 at 50iterations 0.7220012 14.18450 at 60iterations 0.4196120 8.306574 at 70iterations 0.2424423 4.176727 at 80iterations 0.1402151 2.589825 at 90iterations 8.1125662E-02 1.381435 at 100iterations 4.6923775E-02 0.7982292 at 110iterations 2.7087782E-02 0.4588356 at 120iterations 1.5666204E-02 0.2759514 at 130iterations 9.0703489E-03 0.1593227 at 140iterations 5.2507306E-03 9.0087891E-02 at 150iterations 3.0434341E-03 5.1123500E-02 at 160iterations 1.7727315E-03 3.1404674E-02 at 170iterations 1.0385150E-03 1.6628265E-02 at 180iterations finished qdiffx linear iterations at : 14:14:49 total time elapsed so far: 18.62000 # loops : 180 mean,max change (kT/e) : 1.0385150E-03 1.6628265E-02 energy calculations done at 18.62000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.79000 DelPhi exited at 14:14:50 18.794u 0.504s 0:19.57 98.5% 0+0k 0+0io 0pf+0w