Sun Oct 9 13:10:27 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 Sun Oct 9 2011 at 13:10:27 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 = 2343 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: 0.6967686 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): -6.013000 44.44900 ymin,ymax (A): -14.36400 36.72900 zmin,zma (A): 2.317000 44.56700 x,y,z range (A): 50.46200 51.09300 42.25000 scale (grids/A): 0.6967686 object centre (A): 19.21800 11.18250 23.44200 number of atom coordinates read : 2343 total number of charged atoms : 2203 net assigned charge : 4.500011 assigned positive charge : 356.5711 centred at (gu) : 89.36666 91.18996 90.87039 assigned negative charge : -352.0716 centred at (gu) : 89.38009 91.31561 90.92068 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 7943 nv = 96 ne = 84 npr = 45762 no. pairs analyzed = 45762 no. exposed pairs = 3035 no. arc points = 20997 no. surface atoms = 1011 nbur = 1332 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 533 mr = 4486 m= 1 mr = 74 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 number of dielectric boundary points 3917 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1952 ## 213 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 8742 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.4008843E-08 9.4039843E-09 midg,1,midg; midg,igrid,midg 6.6845267E-08 -3.2841026E-08 1,midg,midg; igrid,midg,midg 4.0842032E-08 2.1664555E-08 gauss-seidel spectral radius is 0.9892989 estimated iterations to convergence 79 setup time was (sec) 0.5900000 now iterating at: 13:10:28 rms-change max change #iterations 0.2013067 32.72655 at 10iterations 2.4570180E-02 3.222324 at 20iterations 3.4998362E-03 0.4752350 at 30iterations 8.1136165E-04 0.1412582 at 40iterations 2.7190731E-04 4.5269012E-02 at 50iterations finished qdiffx linear iterations at : 13:10:32 total time elapsed so far: 5.010000 # loops : 50 mean,max change (kT/e) : 2.7190731E-04 4.5269012E-02 energy calculations done at 5.010000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.180000 DelPhi exited at 13:10:33 5.183u 0.440s 0:05.89 95.4% 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 13:10:33 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 = 2343 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: 2.090306 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): -6.013000 44.44900 ymin,ymax (A): -14.36400 36.72900 zmin,zma (A): 2.317000 44.56700 x,y,z range (A): 50.46200 51.09300 42.25000 scale (grids/A): 2.090306 object centre (A): 19.21800 11.18250 23.44200 number of atom coordinates read : 2343 total number of charged atoms : 2203 net assigned charge : 4.500011 assigned positive charge : 356.5711 centred at (gu) : 88.09958 93.56924 92.61065 assigned negative charge : -352.0716 centred at (gu) : 88.14001 93.94677 92.76191 start vw surface at 0.1000000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 84188 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20997 grid for indexing accessible points = 1.400000 m= 34458 mr = 59047 m= 6467 mr = 25894 m= 544 mr = 4227 m= 17 mr = 281 m= 1 mr = 2 m= 0 mr = 0 time to grow re-entrant surface = 0.3900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7000000 number of dielectric boundary points 36224 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 104 iepsmp to db, and charging done at 0.8300000 number of grid points assigned charge 17477 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) : 0.6967686 object centre at (A) : 19.21800 11.18250 23.44200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.5487814E-02 1.2574006E-02 midg,1,midg; midg,igrid,midg 2.0166034E-02 -3.4815971E-02 1,midg,midg; igrid,midg,midg 5.8098353E-02 -1.5232097E-02 gauss-seidel spectral radius is 0.9988366 estimated iterations to convergence 232 setup time was (sec) 1.050000 now iterating at: 13:10:35 rms-change max change #iterations 4.818662 215.2088 at 10iterations 2.372519 77.03851 at 20iterations 1.174787 34.26278 at 30iterations 0.5829957 18.51047 at 40iterations 0.2901080 8.706703 at 50iterations 0.1441376 4.270210 at 60iterations 7.1767218E-02 1.933503 at 70iterations 3.5865139E-02 1.086543 at 80iterations 1.7936192E-02 0.5797577 at 90iterations 9.0877702E-03 0.2910261 at 100iterations 4.6585165E-03 0.1384659 at 110iterations 2.4699955E-03 7.9364777E-02 at 120iterations finished qdiffx linear iterations at : 13:10:47 total time elapsed so far: 13.42000 # loops : 120 mean,max change (kT/e) : 2.4699955E-03 7.9364777E-02 energy calculations done at 13.42000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.57000 DelPhi exited at 13:10:47 13.571u 0.549s 0:14.43 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 Sun Oct 9 2011 at 13:10:47 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 = 2343 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: 3.135459 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): -6.013000 44.44900 ymin,ymax (A): -14.36400 36.72900 zmin,zma (A): 2.317000 44.56700 x,y,z range (A): 50.46200 51.09300 42.25000 scale (grids/A): 3.135459 object centre (A): 19.21800 11.18250 23.44200 number of atom coordinates read : 2343 total number of charged atoms : 2203 net assigned charge : 4.500011 assigned positive charge : 356.5711 centred at (gu) : 87.14931 95.35382 93.91578 assigned negative charge : -352.0716 centred at (gu) : 87.20995 95.92002 94.14285 start vw surface at 0.1200000 fill in re-entrant regions at 0.8700000 boundary points on vw surface= 193688 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20997 grid for indexing accessible points = 1.400000 m= 106290 mr = 141701 m= 43669 mr = 88000 m= 12142 mr = 35775 m= 2309 mr = 9325 m= 303 mr = 1643 m= 24 mr = 218 m= 0 mr = 18 time to grow re-entrant surface = 1.250000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.260000 number of dielectric boundary points 81745 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.430000 number of grid points assigned charge 17624 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) : 2.090306 object centre at (A) : 19.21800 11.18250 23.44200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4304032 -1.4243267E-02 midg,1,midg; midg,igrid,midg 0.3227007 -0.5159274 1,midg,midg; igrid,midg,midg 0.5536576 -0.4505198 gauss-seidel spectral radius is 0.9993008 estimated iterations to convergence 298 setup time was (sec) 2.670000 now iterating at: 13:10:51 rms-change max change #iterations 10.90385 429.7965 at 10iterations 6.492234 129.1955 at 20iterations 3.860753 79.14391 at 30iterations 2.288445 42.75603 at 40iterations 1.356110 23.43306 at 50iterations 0.7987650 14.29135 at 60iterations 0.4711471 9.292522 at 70iterations 0.2770738 5.185891 at 80iterations 0.1628568 2.963490 at 90iterations 9.5731713E-02 1.598734 at 100iterations 5.6379236E-02 0.9844122 at 110iterations 3.3350267E-02 0.5795803 at 120iterations 1.9861136E-02 0.3570709 at 130iterations 1.2017442E-02 0.2205999 at 140iterations 7.4936845E-03 0.1406021 at 150iterations 4.8777098E-03 0.1010590 at 160iterations 3.3726105E-03 6.9992065E-02 at 170iterations 2.4830024E-03 5.2627563E-02 at 180iterations finished qdiffx linear iterations at : 13:11:11 total time elapsed so far: 23.43000 # loops : 180 mean,max change (kT/e) : 2.4830024E-03 5.2627563E-02 energy calculations done at 23.43000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 23.60000 DelPhi exited at 13:11:12 23.602u 0.518s 0:24.43 98.6% 0+0k 0+0io 0pf+0w