Sat Oct 15 15:12:32 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 Sat Oct 15 2011 at 15:12:32 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 = 3132 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.6009250 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): -31.28200 26.16500 ymin,ymax (A): 17.94200 77.18400 zmin,zma (A): -20.45800 34.67500 x,y,z range (A): 57.44700 59.24200 55.13300 scale (grids/A): 0.6009250 object centre (A): -2.558499 47.56300 7.108500 number of atom coordinates read : 3132 total number of charged atoms : 2976 net assigned charge : -1.499987 assigned positive charge : 471.6571 centred at (gu) : 89.50398 88.53450 90.51619 assigned negative charge : -473.1583 centred at (gu) : 89.54527 88.76182 90.59300 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7421 nv = 96 ne = 84 npr = 62003 no. pairs analyzed = 62003 no. exposed pairs = 4447 no. arc points = 30222 no. surface atoms = 1484 nbur = 1648 mkacc time = 0.1700000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 370 mr = 3641 m= 1 mr = 35 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3900000 number of dielectric boundary points 4116 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3038 ## 306 charges are in solution ## iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 9332 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.3692341E-09 -4.8963757E-09 midg,1,midg; midg,igrid,midg 1.3114457E-08 -8.2069640E-09 1,midg,midg; igrid,midg,midg 1.2054650E-09 -2.4144000E-09 gauss-seidel spectral radius is 0.9857185 estimated iterations to convergence 69 setup time was (sec) 0.6800000 now iterating at: 15:12:33 rms-change max change #iterations 0.1168024 17.16935 at 10iterations 9.8450091E-03 1.665538 at 20iterations 8.4104756E-04 0.1268501 at 30iterations 7.8832760E-05 1.1232376E-02 at 40iterations 1.2303369E-05 2.4104118E-03 at 50iterations finished qdiffx linear iterations at : 15:12:37 total time elapsed so far: 4.100000 # loops : 50 mean,max change (kT/e) : 1.2303369E-05 2.4104118E-03 energy calculations done at 4.100000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.290000 DelPhi exited at 15:12:37 4.292u 0.296s 0:04.97 92.1% 0+0k 0+0io 6pf+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 Sat Oct 15 2011 at 15:12:37 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 = 3132 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.802775 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): -31.28200 26.16500 ymin,ymax (A): 17.94200 77.18400 zmin,zma (A): -20.45800 34.67500 x,y,z range (A): 57.44700 59.24200 55.13300 scale (grids/A): 1.802775 object centre (A): -2.558499 47.56300 7.108500 number of atom coordinates read : 3132 total number of charged atoms : 2976 net assigned charge : -1.499987 assigned positive charge : 471.6571 centred at (gu) : 88.51152 85.60291 91.54784 assigned negative charge : -473.1583 centred at (gu) : 88.63556 86.28514 91.77838 start vw surface at 0.1700000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 79599 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30222 grid for indexing accessible points = 1.400000 m= 26794 mr = 51693 m= 3678 mr = 18365 m= 163 mr = 1931 m= 1 mr = 31 m= 0 mr = 0 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7300000 number of dielectric boundary points 38215 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 247 iepsmp to db, and charging done at 0.8800000 number of grid points assigned charge 23209 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) : 0.6009250 object centre at (A) : -2.558499 47.56300 7.108500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.4464692E-02 -4.1955961E-03 midg,1,midg; midg,igrid,midg 3.2083862E-02 -4.1157439E-02 1,midg,midg; igrid,midg,midg 8.2380539E-03 -2.1894269E-02 gauss-seidel spectral radius is 0.9985408 estimated iterations to convergence 208 setup time was (sec) 1.050000 now iterating at: 15:12:39 rms-change max change #iterations 4.196579 201.2841 at 10iterations 1.906077 70.41518 at 20iterations 0.8622373 29.11716 at 30iterations 0.3937103 12.13644 at 40iterations 0.1784815 6.003124 at 50iterations 8.1320964E-02 2.604135 at 60iterations 3.7160687E-02 1.111143 at 70iterations 1.6889524E-02 0.5118554 at 80iterations 7.6897913E-03 0.2378273 at 90iterations 3.5187008E-03 0.1113167 at 100iterations 1.6040539E-03 4.8810005E-02 at 110iterations 7.3515630E-04 2.4043083E-02 at 120iterations finished qdiffx linear iterations at : 15:12:48 total time elapsed so far: 9.850000 # loops : 120 mean,max change (kT/e) : 7.3515630E-04 2.4043083E-02 energy calculations done at 9.850000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.03000 DelPhi exited at 15:12:48 10.032u 0.343s 0:10.72 96.7% 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 Sat Oct 15 2011 at 15:12:48 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 = 3132 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.704163 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): -31.28200 26.16500 ymin,ymax (A): 17.94200 77.18400 zmin,zma (A): -20.45800 34.67500 x,y,z range (A): 57.44700 59.24200 55.13300 scale (grids/A): 2.704163 object centre (A): -2.558499 47.56300 7.108500 number of atom coordinates read : 3132 total number of charged atoms : 2976 net assigned charge : -1.499987 assigned positive charge : 471.6571 centred at (gu) : 87.76707 83.40408 92.32159 assigned negative charge : -473.1583 centred at (gu) : 87.95338 84.42768 92.66750 start vw surface at 0.1700000 fill in re-entrant regions at 0.6000000 boundary points on vw surface= 184039 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30222 grid for indexing accessible points = 1.400000 m= 87739 mr = 126861 m= 29708 mr = 68287 m= 6128 mr = 22467 m= 722 mr = 4138 m= 31 mr = 416 m= 0 mr = 6 time to grow re-entrant surface = 1.120000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.850000 number of dielectric boundary points 86192 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 2.020000 number of grid points assigned charge 23804 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) : 1.802775 object centre at (A) : -2.558499 47.56300 7.108500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1469003 1.0043290E-02 midg,1,midg; midg,igrid,midg 0.3591887 -0.5869933 1,midg,midg; igrid,midg,midg 0.1635332 -0.2742028 gauss-seidel spectral radius is 0.9992544 estimated iterations to convergence 289 setup time was (sec) 2.210000 now iterating at: 15:12:51 rms-change max change #iterations 10.36168 345.3349 at 10iterations 6.130805 145.3722 at 20iterations 3.583366 84.01358 at 30iterations 2.089403 45.76371 at 40iterations 1.214845 24.06744 at 50iterations 0.7024497 13.94758 at 60iterations 0.4068726 7.425056 at 70iterations 0.2343357 4.581348 at 80iterations 0.1352119 2.559149 at 90iterations 7.7780142E-02 1.421192 at 100iterations 4.4668920E-02 0.8572474 at 110iterations 2.5762066E-02 0.4521976 at 120iterations 1.4764558E-02 0.2797501 at 130iterations 8.4845871E-03 0.1543608 at 140iterations 4.8855953E-03 8.7743282E-02 at 150iterations 2.8127187E-03 5.1647186E-02 at 160iterations 1.6286086E-03 3.1669617E-02 at 170iterations 9.4844296E-04 2.0478129E-02 at 180iterations finished qdiffx linear iterations at : 15:13:06 total time elapsed so far: 17.11000 # loops : 180 mean,max change (kT/e) : 9.4844296E-04 2.0478129E-02 energy calculations done at 17.11000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.30000 DelPhi exited at 15:13:06 17.303u 0.343s 0:18.05 97.7% 0+0k 0+0io 0pf+0w