Mon Oct 10 10:23:42 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 10:23:42 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: 256 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2751 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5940461 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): 20.21600 80.14400 ymin,ymax (A): 33.36300 88.51800 zmin,zma (A): -1.497000 50.18200 x,y,z range (A): 59.92801 55.15500 51.67900 scale (grids/A): 0.5940461 object centre (A): 50.18000 60.94050 24.34250 number of atom coordinates read : 2751 total number of charged atoms : 2607 net assigned charge : 11.00002 assigned positive charge : 402.8361 centred at (gu) : 87.56494 88.03249 86.86485 assigned negative charge : -391.8365 centred at (gu) : 87.49027 88.06310 86.78274 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 6591 nv = 96 ne = 84 npr = 53730 no. pairs analyzed = 53730 no. exposed pairs = 4034 no. arc points = 28841 no. surface atoms = 1337 nbur = 1414 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 347 mr = 3065 m= 4 mr = 27 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 3850 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2793 ## 260 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 8136 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.7382323E-09 3.1603389E-09 midg,1,midg; midg,igrid,midg 7.5291400E-09 1.9603694E-09 1,midg,midg; igrid,midg,midg 2.7717868E-09 3.5588275E-09 gauss-seidel spectral radius is 0.9853633 estimated iterations to convergence 68 setup time was (sec) 0.6100000 now iterating at: 10:23:43 rms-change max change #iterations 0.1020624 19.29712 at 10iterations 8.4502017E-03 1.328619 at 20iterations 7.1497518E-04 9.7965240E-02 at 30iterations 7.1498071E-05 9.9383593E-03 at 40iterations 1.0621492E-05 1.3122559E-03 at 50iterations finished qdiffx linear iterations at : 10:23:46 total time elapsed so far: 3.490000 # loops : 50 mean,max change (kT/e) : 1.0621492E-05 1.3122559E-03 energy calculations done at 3.490000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.680000 DelPhi exited at 10:23:46 3.684u 0.203s 0:04.25 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 Mon Oct 10 2011 at 10:23:46 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: 256 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2751 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.782138 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): 20.21600 80.14400 ymin,ymax (A): 33.36300 88.51800 zmin,zma (A): -1.497000 50.18200 x,y,z range (A): 59.92801 55.15500 51.67900 scale (grids/A): 1.782138 object centre (A): 50.18000 60.94050 24.34250 number of atom coordinates read : 2751 total number of charged atoms : 2607 net assigned charge : 11.00002 assigned positive charge : 402.8361 centred at (gu) : 82.69450 84.09724 80.59403 assigned negative charge : -391.8365 centred at (gu) : 82.47041 84.18927 80.34817 start vw surface at 0.1700000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 70714 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28841 grid for indexing accessible points = 1.400000 m= 22721 mr = 44581 m= 2930 mr = 14815 m= 128 mr = 1389 m= 3 mr = 20 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5600000 number of dielectric boundary points 35691 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 229 iepsmp to db, and charging done at 0.6900000 number of grid points assigned charge 20310 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) : 0.5940461 object centre at (A) : 50.18000 60.94050 24.34250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.5555442E-03 8.8806348E-03 midg,1,midg; midg,igrid,midg 3.2208566E-02 1.6981840E-02 1,midg,midg; igrid,midg,midg 3.2624077E-02 1.9066375E-02 gauss-seidel spectral radius is 0.9984653 estimated iterations to convergence 202 setup time was (sec) 0.8800000 now iterating at: 10:23:48 rms-change max change #iterations 3.748863 155.6973 at 10iterations 1.670781 64.96948 at 20iterations 0.7427921 26.07548 at 30iterations 0.3313623 12.18104 at 40iterations 0.1475214 5.420002 at 50iterations 6.5924108E-02 2.234024 at 60iterations 2.9442355E-02 1.005699 at 70iterations 1.3098498E-02 0.4340572 at 80iterations 5.8680312E-03 0.1948395 at 90iterations 2.6170709E-03 9.9663734E-02 at 100iterations 1.1703551E-03 4.0692806E-02 at 110iterations 5.2473362E-04 1.9958496E-02 at 120iterations finished qdiffx linear iterations at : 10:23:55 total time elapsed so far: 8.080000 # loops : 120 mean,max change (kT/e) : 5.2473362E-04 1.9958496E-02 energy calculations done at 8.080000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.260000 DelPhi exited at 10:23:56 8.267u 0.271s 0:09.06 94.1% 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 10:23:56 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: 256 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2751 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: 2.673208 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): 20.21600 80.14400 ymin,ymax (A): 33.36300 88.51800 zmin,zma (A): -1.497000 50.18200 x,y,z range (A): 59.92801 55.15500 51.67900 scale (grids/A): 2.673208 object centre (A): 50.18000 60.94050 24.34250 number of atom coordinates read : 2751 total number of charged atoms : 2607 net assigned charge : 11.00002 assigned positive charge : 402.8361 centred at (gu) : 79.04167 81.14577 75.89082 assigned negative charge : -391.8365 centred at (gu) : 78.70551 81.28384 75.52216 start vw surface at 0.1500000 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 163519 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28841 grid for indexing accessible points = 1.400000 m= 75045 mr = 109904 m= 24315 mr = 56991 m= 4828 mr = 17552 m= 486 mr = 3038 m= 13 mr = 191 m= 0 mr = 0 time to grow re-entrant surface = 0.7800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.350000 number of dielectric boundary points 80530 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.500000 number of grid points assigned charge 20852 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) : 1.782138 object centre at (A) : 50.18000 60.94050 24.34250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.4936030E-02 7.9249434E-02 midg,1,midg; midg,igrid,midg 0.3578897 0.2007101 1,midg,midg; igrid,midg,midg 0.3924045 0.4721456 gauss-seidel spectral radius is 0.9992290 estimated iterations to convergence 284 setup time was (sec) 1.700000 now iterating at: 10:23:57 rms-change max change #iterations 9.607700 289.5299 at 10iterations 5.766625 159.9804 at 20iterations 3.393473 99.06504 at 30iterations 1.980789 52.51788 at 40iterations 1.145506 27.27673 at 50iterations 0.6613209 16.64571 at 60iterations 0.3800575 9.118219 at 70iterations 0.2176132 4.966469 at 80iterations 0.1248472 2.715496 at 90iterations 7.1379356E-02 1.532547 at 100iterations 4.0682133E-02 0.9238649 at 110iterations 2.3186302E-02 0.4770994 at 120iterations 1.3237346E-02 0.3027172 at 130iterations 7.5287381E-03 0.1602993 at 140iterations 4.2830738E-03 0.1021404 at 150iterations 2.4353112E-03 5.4233551E-02 at 160iterations 1.3871903E-03 3.1415939E-02 at 170iterations 7.8963465E-04 1.6613007E-02 at 180iterations finished qdiffx linear iterations at : 10:24:09 total time elapsed so far: 13.39000 # loops : 180 mean,max change (kT/e) : 7.8963465E-04 1.6613007E-02 energy calculations done at 13.39000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.57000 DelPhi exited at 10:24:10 13.567u 0.276s 0:14.23 97.1% 0+0k 0+0io 0pf+0w