Wed Dec 21 14:22:12 PST 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 Wed Dec 21 2011 at 14:22:14 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: 288 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1978 !!! WARNING: HIQ 147 has a net charge of 0.5140 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: 0.6495638 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): 26.88500 64.71400 ymin,ymax (A): -7.749000 45.55500 zmin,zma (A): 39.86500 94.67101 x,y,z range (A): 37.82899 53.30400 54.80601 scale (grids/A): 0.6495638 object centre (A): 45.79950 18.90300 67.26801 number of atom coordinates read : 1978 total number of charged atoms : 1846 net assigned charge : 2.514006 assigned positive charge : 293.8099 centred at (gu) : 89.83674 88.51180 89.97375 assigned negative charge : -291.2962 centred at (gu) : 89.96638 88.37527 90.05489 start vw surface at 0.1600000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 5783 nv = 96 ne = 84 npr = 40947 no. pairs analyzed = 40947 no. exposed pairs = 2440 no. arc points = 17195 no. surface atoms = 837 nbur = 1141 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 342 mr = 3253 m= 6 mr = 64 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 2814 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1736 ## 137 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 6662 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.4201601E-08 -4.1735713E-09 midg,1,midg; midg,igrid,midg -1.4775514E-08 1.4788668E-08 1,midg,midg; igrid,midg,midg 2.0164537E-08 -9.4532719E-09 gauss-seidel spectral radius is 0.9876638 estimated iterations to convergence 74 setup time was (sec) 0.6200000 now iterating at: 14:22:16 rms-change max change #iterations 0.1370445 23.26111 at 10iterations 1.3774689E-02 2.133229 at 20iterations 1.4297367E-03 0.2594376 at 30iterations 1.4567772E-04 2.6412964E-02 at 40iterations 1.4675365E-05 2.1266937E-03 at 50iterations finished qdiffx linear iterations at : 14:22:20 total time elapsed so far: 4.860000 # loops : 50 mean,max change (kT/e) : 1.4675365E-05 2.1266937E-03 energy calculations done at 4.860000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.040000 DelPhi exited at 14:22:31 5.044u 0.331s 0:17.12 31.3% 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 Wed Dec 21 2011 at 14:22:33 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: 288 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1978 !!! WARNING: HIQ 147 has a net charge of 0.5140 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: 1.948691 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): 26.88500 64.71400 ymin,ymax (A): -7.749000 45.55500 zmin,zma (A): 39.86500 94.67101 x,y,z range (A): 37.82899 53.30400 54.80601 scale (grids/A): 1.948691 object centre (A): 45.79950 18.90300 67.26801 number of atom coordinates read : 1978 total number of charged atoms : 1846 net assigned charge : 2.514006 assigned positive charge : 293.8099 centred at (gu) : 89.50998 85.53525 89.92117 assigned negative charge : -291.2962 centred at (gu) : 89.89935 85.12601 90.16491 start vw surface at 0.1300000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 60903 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17195 grid for indexing accessible points = 1.400000 m= 23804 mr = 42121 m= 4200 mr = 18480 m= 283 mr = 2827 m= 6 mr = 136 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 404 time to turn everything in is 0.5800000 number of dielectric boundary points 25632 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 96 iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 14555 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) : 0.6495638 object centre at (A) : 45.79950 18.90300 67.26801 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.6888155E-03 2.0991333E-02 midg,1,midg; midg,igrid,midg -1.2558955E-02 4.0451720E-02 1,midg,midg; igrid,midg,midg 1.5702948E-02 -4.5587518E-03 gauss-seidel spectral radius is 0.9986198 estimated iterations to convergence 213 setup time was (sec) 0.9400000 now iterating at: 14:22:35 rms-change max change #iterations 3.773791 177.3087 at 10iterations 1.765474 69.01146 at 20iterations 0.8216622 28.38546 at 30iterations 0.3847050 13.87462 at 40iterations 0.1792141 5.972977 at 50iterations 8.3542831E-02 2.974213 at 60iterations 3.8906988E-02 1.357407 at 70iterations 1.8156862E-02 0.6749153 at 80iterations 8.4389159E-03 0.3101196 at 90iterations 3.9244108E-03 0.1366901 at 100iterations 1.8370909E-03 6.3241959E-02 at 110iterations 8.5918995E-04 2.7763367E-02 at 120iterations finished qdiffx linear iterations at : 14:22:45 total time elapsed so far: 11.60000 # loops : 120 mean,max change (kT/e) : 8.5918995E-04 2.7763367E-02 energy calculations done at 11.60000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.76000 DelPhi exited at 14:22:51 11.763u 0.502s 0:18.75 65.3% 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 Wed Dec 21 2011 at 14:22:51 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: 288 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1978 !!! WARNING: HIQ 147 has a net charge of 0.5140 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: 2.923037 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): 26.88500 64.71400 ymin,ymax (A): -7.749000 45.55500 zmin,zma (A): 39.86500 94.67101 x,y,z range (A): 37.82899 53.30400 54.80601 scale (grids/A): 2.923037 object centre (A): 45.79950 18.90300 67.26801 number of atom coordinates read : 1978 total number of charged atoms : 1846 net assigned charge : 2.514006 assigned positive charge : 293.8099 centred at (gu) : 89.26501 83.30299 89.88165 assigned negative charge : -291.2962 centred at (gu) : 89.84915 82.68905 90.24735 start vw surface at 0.1400000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 140483 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17195 grid for indexing accessible points = 1.400000 m= 74804 mr = 101741 m= 30183 mr = 62575 m= 7716 mr = 25416 m= 1227 mr = 6072 m= 97 mr = 891 m= 1 mr = 52 m= 0 mr = 0 time to grow re-entrant surface = 0.8800001 no. cavity mid-points inaccessible to solvent = 1529 time to turn everything in is 1.480000 number of dielectric boundary points 57764 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.650000 number of grid points assigned charge 14768 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) : 1.948691 object centre at (A) : 45.79950 18.90300 67.26801 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.6659175E-02 0.2128086 midg,1,midg; midg,igrid,midg -0.2025362 0.3828329 1,midg,midg; igrid,midg,midg 0.1292123 -3.4342837E-02 gauss-seidel spectral radius is 0.9992418 estimated iterations to convergence 287 setup time was (sec) 1.880000 now iterating at: 14:22:55 rms-change max change #iterations 8.834634 423.8322 at 10iterations 5.102973 139.7786 at 20iterations 2.927037 59.29678 at 30iterations 1.679240 34.81781 at 40iterations 0.9631349 20.30735 at 50iterations 0.5504544 10.79642 at 60iterations 0.3145293 6.918559 at 70iterations 0.1796425 3.684798 at 80iterations 0.1023827 2.320608 at 90iterations 5.8393806E-02 1.191654 at 100iterations 3.3345446E-02 0.6333694 at 110iterations 1.9022007E-02 0.3690300 at 120iterations 1.0831167E-02 0.2107372 at 130iterations 6.2060370E-03 0.1416941 at 140iterations 3.5325005E-03 7.7878952E-02 at 150iterations 2.0071494E-03 3.8241386E-02 at 160iterations 1.1443881E-03 2.1429300E-02 at 170iterations 6.5340271E-04 1.2342453E-02 at 180iterations finished qdiffx linear iterations at : 14:23:13 total time elapsed so far: 19.65000 # loops : 180 mean,max change (kT/e) : 6.5340271E-04 1.2342453E-02 energy calculations done at 19.65000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.82000 DelPhi exited at 14:23:15 19.824u 0.522s 0:23.76 85.6% 0+0k 0+0io 0pf+0w