Mon Oct 10 19:33:04 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 Mon Oct 10 2011 at 19:33:04 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: 241 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3151 !!! WARNING: WAT 3 has a net charge of -0.8340 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5911264 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): 14.06800 71.66300 ymin,ymax (A): -0.3980000 54.17100 zmin,zma (A): 6.795000 67.01900 x,y,z range (A): 57.59500 54.56900 60.22401 scale (grids/A): 0.5911264 object centre (A): 42.86550 26.88650 36.90700 number of atom coordinates read : 3151 total number of charged atoms : 3006 net assigned charge : -7.333985 assigned positive charge : 471.4156 centred at (gu) : 89.60385 90.73277 91.37170 assigned negative charge : -478.7509 centred at (gu) : 89.56677 90.85835 91.46397 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 7297 nv = 96 ne = 84 npr = 62956 no. pairs analyzed = 62956 no. exposed pairs = 4158 no. arc points = 29393 no. surface atoms = 1399 nbur = 1752 mkacc time = 0.1400000 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 = 1.484000 m= 323 mr = 3731 m= 1 mr = 26 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 11 time to turn everything in is 0.3700000 number of dielectric boundary points 3864 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2909 ## 295 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 9194 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.9432714E-10 -7.4310544E-09 midg,1,midg; midg,igrid,midg 1.6326928E-09 -7.7844442E-09 1,midg,midg; igrid,midg,midg -3.8384940E-09 -9.1307689E-10 gauss-seidel spectral radius is 0.9852464 estimated iterations to convergence 68 setup time was (sec) 0.6300000 now iterating at: 19:33:05 rms-change max change #iterations 0.1105111 16.34949 at 10iterations 9.0966392E-03 1.374648 at 20iterations 7.3868711E-04 0.1125946 at 30iterations 6.0749844E-05 8.5735321E-03 at 40iterations 5.0374651E-06 8.3470345E-04 at 50iterations finished qdiffx linear iterations at : 19:33:08 total time elapsed so far: 3.450000 # loops : 50 mean,max change (kT/e) : 5.0374651E-06 8.3470345E-04 energy calculations done at 3.450000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.660000 DelPhi exited at 19:33:10 3.662u 0.187s 0:05.29 72.5% 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 19:33:10 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: 241 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3151 !!! WARNING: WAT 3 has a net charge of -0.8340 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.773379 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): 14.06800 71.66300 ymin,ymax (A): -0.3980000 54.17100 zmin,zma (A): 6.795000 67.01900 x,y,z range (A): 57.59500 54.56900 60.22401 scale (grids/A): 1.773379 object centre (A): 42.86550 26.88650 36.90700 number of atom coordinates read : 3151 total number of charged atoms : 3006 net assigned charge : -7.333985 assigned positive charge : 471.4156 centred at (gu) : 88.81055 92.19734 94.11449 assigned negative charge : -478.7509 centred at (gu) : 88.69993 92.57461 94.39141 start vw surface at 0.2000000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 79825 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29393 grid for indexing accessible points = 1.400000 m= 25201 mr = 53379 m= 2997 mr = 17431 m= 111 mr = 1563 m= 0 mr = 22 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 880 time to turn everything in is 0.6200000 number of dielectric boundary points 35739 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 242 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 23425 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) : 0.5911264 object centre at (A) : 42.86550 26.88650 36.90700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.6683988E-02 1.1232378E-03 midg,1,midg; midg,igrid,midg -1.3315900E-03 -2.4503585E-02 1,midg,midg; igrid,midg,midg -3.9570309E-02 1.2596792E-02 gauss-seidel spectral radius is 0.9984912 estimated iterations to convergence 204 setup time was (sec) 0.8900000 now iterating at: 19:33:11 rms-change max change #iterations 4.108409 176.0487 at 10iterations 1.838498 69.37930 at 20iterations 0.8232795 30.81423 at 30iterations 0.3715679 12.87217 at 40iterations 0.1667524 6.344274 at 50iterations 7.5057767E-02 2.675875 at 60iterations 3.3664547E-02 1.039476 at 70iterations 1.5160576E-02 0.5199280 at 80iterations 6.8338583E-03 0.2224693 at 90iterations 3.0764230E-03 9.5281601E-02 at 100iterations 1.3840911E-03 4.8465252E-02 at 110iterations 6.2520162E-04 2.1701097E-02 at 120iterations finished qdiffx linear iterations at : 19:33:17 total time elapsed so far: 7.340000 # loops : 120 mean,max change (kT/e) : 6.2520162E-04 2.1701097E-02 energy calculations done at 7.340000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.530000 DelPhi exited at 19:33:20 7.532u 0.171s 0:10.61 72.5% 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 19:33:20 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: 241 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3151 !!! WARNING: WAT 3 has a net charge of -0.8340 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: 2.660069 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): 14.06800 71.66300 ymin,ymax (A): -0.3980000 54.17100 zmin,zma (A): 6.795000 67.01900 x,y,z range (A): 57.59500 54.56900 60.22401 scale (grids/A): 2.660069 object centre (A): 42.86550 26.88650 36.90700 number of atom coordinates read : 3151 total number of charged atoms : 3006 net assigned charge : -7.333985 assigned positive charge : 471.4156 centred at (gu) : 88.21559 93.29576 96.17136 assigned negative charge : -478.7509 centred at (gu) : 88.04988 93.86179 96.58698 start vw surface at 0.1800000 fill in re-entrant regions at 0.5000000 boundary points on vw surface= 185195 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29393 grid for indexing accessible points = 1.400000 m= 85474 mr = 130688 m= 26316 mr = 67365 m= 4752 mr = 20011 m= 464 mr = 3193 m= 13 mr = 253 m= 0 mr = 5 time to grow re-entrant surface = 0.8099999 no. cavity mid-points inaccessible to solvent = 3033 time to turn everything in is 1.430000 number of dielectric boundary points 80699 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 6 iepsmp to db, and charging done at 1.570000 number of grid points assigned charge 24038 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) : 1.773379 object centre at (A) : 42.86550 26.88650 36.90700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2747634 0.2116770 midg,1,midg; midg,igrid,midg -2.0810720E-02 -0.2086070 1,midg,midg; igrid,midg,midg -0.4803257 0.2673798 gauss-seidel spectral radius is 0.9992439 estimated iterations to convergence 287 setup time was (sec) 1.740000 now iterating at: 19:33:22 rms-change max change #iterations 10.22811 325.7614 at 10iterations 6.014624 159.8582 at 20iterations 3.496303 93.59695 at 30iterations 2.025015 50.71561 at 40iterations 1.168810 24.23551 at 50iterations 0.6719909 13.56230 at 60iterations 0.3862263 7.903749 at 70iterations 0.2212913 4.103582 at 80iterations 0.1266092 2.633758 at 90iterations 7.2275229E-02 1.325558 at 100iterations 4.1331362E-02 0.7351499 at 110iterations 2.3661988E-02 0.4697676 at 120iterations 1.3533334E-02 0.2377639 at 130iterations 7.7155801E-03 0.1424294 at 140iterations 4.4015669E-03 7.8273773E-02 at 150iterations 2.5119856E-03 4.3523431E-02 at 160iterations 1.4361563E-03 2.5680542E-02 at 170iterations 8.2160230E-04 1.4118195E-02 at 180iterations finished qdiffx linear iterations at : 19:33:33 total time elapsed so far: 12.10000 # loops : 180 mean,max change (kT/e) : 8.2160230E-04 1.4118195E-02 energy calculations done at 12.10000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.31000 DelPhi exited at 19:33:34 12.317u 0.181s 0:13.52 92.3% 0+0k 0+0io 0pf+0w