Tue Oct 11 07:35:37 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 Tue Oct 11 2011 at 07:35:37 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2380 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: 0.6430171 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): -1.614000 53.75000 ymin,ymax (A): -23.12500 25.88300 zmin,zma (A): 8.990000 54.60800 x,y,z range (A): 55.36400 49.00800 45.61800 scale (grids/A): 0.6430171 object centre (A): 26.06800 1.379000 31.79900 number of atom coordinates read : 2380 total number of charged atoms : 2244 net assigned charge : 5.500007 assigned positive charge : 357.6723 centred at (gu) : 88.63741 89.46938 90.01435 assigned negative charge : -352.1728 centred at (gu) : 88.65694 89.40934 89.82845 start vw surface at 7.9999998E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 6678 nv = 96 ne = 84 npr = 47581 no. pairs analyzed = 47581 no. exposed pairs = 2884 no. arc points = 20595 no. surface atoms = 981 nbur = 1399 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 359 mr = 3715 m= 0 mr = 35 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1800000 number of dielectric boundary points 3287 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2037 ## 229 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 7875 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.2970971E-08 2.9719541E-08 midg,1,midg; midg,igrid,midg 1.9695408E-09 1.3934894E-08 1,midg,midg; igrid,midg,midg 1.4604205E-08 4.9448219E-09 gauss-seidel spectral radius is 0.9874498 estimated iterations to convergence 73 setup time was (sec) 0.3700000 now iterating at: 07:35:38 rms-change max change #iterations 0.1462252 20.27084 at 10iterations 1.4315006E-02 2.693413 at 20iterations 1.5335467E-03 0.2122669 at 30iterations 1.7401863E-04 2.5615692E-02 at 40iterations 2.3414488E-05 3.1280518E-03 at 50iterations finished qdiffx linear iterations at : 07:35:41 total time elapsed so far: 3.210000 # loops : 50 mean,max change (kT/e) : 2.3414488E-05 3.1280518E-03 energy calculations done at 3.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.330000 DelPhi exited at 07:35:42 3.337u 0.181s 0:04.11 85.4% 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 Tue Oct 11 2011 at 07:35:42 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2380 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: 1.929051 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): -1.614000 53.75000 ymin,ymax (A): -23.12500 25.88300 zmin,zma (A): 8.990000 54.60800 x,y,z range (A): 55.36400 49.00800 45.61800 scale (grids/A): 1.929051 object centre (A): 26.06800 1.379000 31.79900 number of atom coordinates read : 2380 total number of charged atoms : 2244 net assigned charge : 5.500007 assigned positive charge : 357.6723 centred at (gu) : 85.91196 88.40775 90.04247 assigned negative charge : -352.1728 centred at (gu) : 85.97073 88.22784 89.48519 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 71632 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20595 grid for indexing accessible points = 1.400000 m= 26454 mr = 49812 m= 4077 mr = 19728 m= 252 mr = 2470 m= 4 mr = 92 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 129 time to turn everything in is 0.3400000 number of dielectric boundary points 30317 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 169 iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 17684 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) : 0.6430171 object centre at (A) : 26.06800 1.379000 31.79900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.9930145E-02 4.0523846E-02 midg,1,midg; midg,igrid,midg 7.1533752E-04 4.3849791E-03 1,midg,midg; igrid,midg,midg 2.1320451E-02 2.9571215E-02 gauss-seidel spectral radius is 0.9986502 estimated iterations to convergence 216 setup time was (sec) 0.5500000 now iterating at: 07:35:42 rms-change max change #iterations 4.091852 208.5958 at 10iterations 1.925632 76.29108 at 20iterations 0.9126692 30.85954 at 30iterations 0.4302138 14.52658 at 40iterations 0.2028405 6.699738 at 50iterations 9.5509008E-02 2.901699 at 60iterations 4.5083087E-02 1.432119 at 70iterations 2.1246688E-02 0.6606874 at 80iterations 9.9965818E-03 0.3355179 at 90iterations 4.7356114E-03 0.1548386 at 100iterations 2.2308177E-03 6.7562103E-02 at 110iterations 1.0553289E-03 3.6319733E-02 at 120iterations finished qdiffx linear iterations at : 07:35:49 total time elapsed so far: 7.460000 # loops : 120 mean,max change (kT/e) : 1.0553289E-03 3.6319733E-02 energy calculations done at 7.460000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.580000 DelPhi exited at 07:35:50 7.587u 0.224s 0:08.55 91.2% 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 Tue Oct 11 2011 at 07:35:50 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2380 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: 2.893577 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): -1.614000 53.75000 ymin,ymax (A): -23.12500 25.88300 zmin,zma (A): 8.990000 54.60800 x,y,z range (A): 55.36400 49.00800 45.61800 scale (grids/A): 2.893577 object centre (A): 26.06800 1.379000 31.79900 number of atom coordinates read : 2380 total number of charged atoms : 2244 net assigned charge : 5.500007 assigned positive charge : 357.6723 centred at (gu) : 83.86783 87.61135 90.06386 assigned negative charge : -352.1728 centred at (gu) : 83.95610 87.34167 89.22779 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 165281 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20595 grid for indexing accessible points = 1.400000 m= 85640 mr = 120178 m= 31046 mr = 70809 m= 7167 mr = 24991 m= 1036 mr = 5183 m= 76 mr = 645 m= 2 mr = 35 m= 0 mr = 0 time to grow re-entrant surface = 0.5300000 no. cavity mid-points inaccessible to solvent = 367 time to turn everything in is 0.9200000 number of dielectric boundary points 68407 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.010000 number of grid points assigned charge 17951 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) : 1.929051 object centre at (A) : 26.06800 1.379000 31.79900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2955844 0.4028624 midg,1,midg; midg,igrid,midg 8.0314102E-03 -3.7158068E-02 1,midg,midg; igrid,midg,midg 0.1042569 0.2697666 gauss-seidel spectral radius is 0.9992564 estimated iterations to convergence 289 setup time was (sec) 1.150000 now iterating at: 07:35:52 rms-change max change #iterations 9.610639 393.5454 at 10iterations 5.600266 192.2921 at 20iterations 3.249093 102.9456 at 30iterations 1.878342 40.73665 at 40iterations 1.086965 22.76315 at 50iterations 0.6252155 12.06460 at 60iterations 0.3603669 6.842022 at 70iterations 0.2071051 3.847422 at 80iterations 0.1191017 2.200768 at 90iterations 6.8520047E-02 1.288034 at 100iterations 3.9280739E-02 0.7147560 at 110iterations 2.2650566E-02 0.4116592 at 120iterations 1.2979567E-02 0.2278557 at 130iterations 7.4659954E-03 0.1330681 at 140iterations 4.3026418E-03 7.5348139E-02 at 150iterations 2.4814210E-03 4.3485641E-02 at 160iterations 1.4436230E-03 2.6786804E-02 at 170iterations 8.4587070E-04 1.8428802E-02 at 180iterations finished qdiffx linear iterations at : 07:36:03 total time elapsed so far: 12.35000 # loops : 180 mean,max change (kT/e) : 8.4587070E-04 1.8428802E-02 energy calculations done at 12.35000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.48000 DelPhi exited at 07:36:04 12.483u 0.219s 0:13.31 95.3% 0+0k 0+0io 0pf+0w