Mon Oct 10 14:12:46 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 14:12:46 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1976 !!! WARNING: CME 167 has a net charge of -0.3480 !!! WARNING: CME 1 has a net charge of -0.1350 !!! WARNING: CME 3 has a net charge of -0.0350 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: 0.6502758 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): -6.106000 30.77500 ymin,ymax (A): -46.52900 7.714000 zmin,zma (A): -54.44900 0.2969999 x,y,z range (A): 36.88100 54.24300 54.74600 scale (grids/A): 0.6502758 object centre (A): 12.33450 -19.40750 -27.07600 number of atom coordinates read : 1976 total number of charged atoms : 1836 net assigned charge : 2.482003 assigned positive charge : 293.2069 centred at (gu) : 90.04196 92.06981 89.87079 assigned negative charge : -290.7253 centred at (gu) : 89.94621 92.20157 89.94168 start vw surface at 0.1400000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 5773 nv = 96 ne = 84 npr = 40063 no. pairs analyzed = 40063 no. exposed pairs = 2565 no. arc points = 17783 no. surface atoms = 871 nbur = 1105 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 342 mr = 3173 m= 0 mr = 55 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2700000 number of dielectric boundary points 2887 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1741 ## 158 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 6665 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.3585782E-08 -2.9259954E-09 midg,1,midg; midg,igrid,midg 1.2987610E-08 -1.6119627E-08 1,midg,midg; igrid,midg,midg -5.8582512E-09 1.6159063E-08 gauss-seidel spectral radius is 0.9876928 estimated iterations to convergence 74 setup time was (sec) 0.4900000 now iterating at: 14:12:47 rms-change max change #iterations 0.1386533 19.87915 at 10iterations 1.3924633E-02 2.010238 at 20iterations 1.4497446E-03 0.2011871 at 30iterations 1.4945610E-04 2.4420738E-02 at 40iterations 1.5088438E-05 2.5024414E-03 at 50iterations finished qdiffx linear iterations at : 14:12:49 total time elapsed so far: 3.140000 # loops : 50 mean,max change (kT/e) : 1.5088438E-05 2.5024414E-03 energy calculations done at 3.140000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.310000 DelPhi exited at 14:12:50 3.316u 0.191s 0:04.07 85.9% 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 Mon Oct 10 2011 at 14:12:50 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1976 !!! WARNING: CME 167 has a net charge of -0.3480 !!! WARNING: CME 1 has a net charge of -0.1350 !!! WARNING: CME 3 has a net charge of -0.0350 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: 1.950827 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): -6.106000 30.77500 ymin,ymax (A): -46.52900 7.714000 zmin,zma (A): -54.44900 0.2969999 x,y,z range (A): 36.88100 54.24300 54.74600 scale (grids/A): 1.950827 object centre (A): 12.33450 -19.40750 -27.07600 number of atom coordinates read : 1976 total number of charged atoms : 1836 net assigned charge : 2.482003 assigned positive charge : 293.2069 centred at (gu) : 90.12561 96.20934 89.61227 assigned negative charge : -290.7253 centred at (gu) : 89.83887 96.60487 89.82520 start vw surface at 0.1500000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 61850 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17783 grid for indexing accessible points = 1.400000 m= 23224 mr = 42449 m= 3897 mr = 17539 m= 245 mr = 2591 m= 3 mr = 91 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 745 time to turn everything in is 0.4700000 number of dielectric boundary points 26549 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 135 iepsmp to db, and charging done at 0.6000000 number of grid points assigned charge 14504 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) : 0.6502758 object centre at (A) : 12.33450 -19.40750 -27.07600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.3611280E-03 4.7704969E-02 midg,1,midg; midg,igrid,midg 4.1269783E-02 -1.2535324E-02 1,midg,midg; igrid,midg,midg -5.1655797E-03 6.6693057E-03 gauss-seidel spectral radius is 0.9986272 estimated iterations to convergence 214 setup time was (sec) 0.7700000 now iterating at: 14:12:51 rms-change max change #iterations 3.815176 181.9546 at 10iterations 1.787086 69.57141 at 20iterations 0.8338868 30.96974 at 30iterations 0.3893189 15.49531 at 40iterations 0.1819994 6.039696 at 50iterations 8.4799141E-02 3.217306 at 60iterations 3.9569944E-02 1.354656 at 70iterations 1.8491140E-02 0.6315684 at 80iterations 8.6605502E-03 0.3313522 at 90iterations 4.0291511E-03 0.1330185 at 100iterations 1.8787460E-03 7.0322514E-02 at 110iterations 8.8067900E-04 3.0944824E-02 at 120iterations finished qdiffx linear iterations at : 14:12:58 total time elapsed so far: 7.370000 # loops : 120 mean,max change (kT/e) : 8.8067900E-04 3.0944824E-02 energy calculations done at 7.370000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.560000 DelPhi exited at 14:12:58 7.559u 0.251s 0:08.16 95.5% 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 14:12:58 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 = 1976 !!! WARNING: CME 167 has a net charge of -0.3480 !!! WARNING: CME 1 has a net charge of -0.1350 !!! WARNING: CME 3 has a net charge of -0.0350 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: 2.926241 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): -6.106000 30.77500 ymin,ymax (A): -46.52900 7.714000 zmin,zma (A): -54.44900 0.2969999 x,y,z range (A): 36.88100 54.24300 54.74600 scale (grids/A): 2.926241 object centre (A): 12.33450 -19.40750 -27.07600 number of atom coordinates read : 1976 total number of charged atoms : 1836 net assigned charge : 2.482003 assigned positive charge : 293.2069 centred at (gu) : 90.18851 99.31398 89.41830 assigned negative charge : -290.7253 centred at (gu) : 89.75837 99.90739 89.73793 start vw surface at 0.1400000 fill in re-entrant regions at 0.4000000 boundary points on vw surface= 142727 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17783 grid for indexing accessible points = 1.400000 m= 73825 mr = 102548 m= 28330 mr = 60980 m= 7207 mr = 23376 m= 1137 mr = 5653 m= 78 mr = 805 m= 3 mr = 46 m= 0 mr = 0 time to grow re-entrant surface = 0.6899999 no. cavity mid-points inaccessible to solvent = 2510 time to turn everything in is 1.200000 number of dielectric boundary points 59899 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.340000 number of grid points assigned charge 14686 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) : 1.950827 object centre at (A) : 12.33450 -19.40750 -27.07600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.2093574E-02 0.8700699 midg,1,midg; midg,igrid,midg 0.4133101 -0.1960137 1,midg,midg; igrid,midg,midg -4.6082981E-02 3.2434288E-02 gauss-seidel spectral radius is 0.9992471 estimated iterations to convergence 288 setup time was (sec) 1.510000 now iterating at: 14:13:00 rms-change max change #iterations 8.911715 398.5440 at 10iterations 5.125245 120.9300 at 20iterations 2.935795 59.87381 at 30iterations 1.683392 35.27356 at 40iterations 0.9615074 18.57911 at 50iterations 0.5486270 12.05588 at 60iterations 0.3132930 5.858774 at 70iterations 0.1785816 3.815598 at 80iterations 0.1019844 1.893976 at 90iterations 5.8204517E-02 1.213688 at 100iterations 3.3269867E-02 0.6527566 at 110iterations 1.9004982E-02 0.3732605 at 120iterations 1.0808025E-02 0.2140045 at 130iterations 6.1835032E-03 0.1307888 at 140iterations 3.5190210E-03 7.0350647E-02 at 150iterations 2.0066511E-03 3.8183689E-02 at 160iterations 1.1501826E-03 2.2026062E-02 at 170iterations 6.5495918E-04 1.2676239E-02 at 180iterations finished qdiffx linear iterations at : 14:13:11 total time elapsed so far: 11.87000 # loops : 180 mean,max change (kT/e) : 6.5495918E-04 1.2676239E-02 energy calculations done at 11.87000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.05000 DelPhi exited at 14:13:11 12.055u 0.242s 0:12.72 96.6% 0+0k 0+0io 0pf+0w