Sun Oct 9 23:14:08 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 23:14:08 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 = 2339 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: 0.6572631 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): -11.81400 31.34100 ymin,ymax (A): -22.34300 31.82100 zmin,zma (A): -9.976000 43.33100 x,y,z range (A): 43.15500 54.16400 53.30700 scale (grids/A): 0.6572631 object centre (A): 9.763500 4.739000 16.67750 number of atom coordinates read : 2339 total number of charged atoms : 2199 net assigned charge : 5.500004 assigned positive charge : 347.7804 centred at (gu) : 92.11576 90.44421 89.81352 assigned negative charge : -342.2808 centred at (gu) : 92.02115 90.31793 89.64709 start vw surface at 0.1400000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 6932 nv = 96 ne = 84 npr = 45970 no. pairs analyzed = 45970 no. exposed pairs = 2947 no. arc points = 20995 no. surface atoms = 1009 nbur = 1330 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 386 mr = 3746 m= 4 mr = 50 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 0.2700000 number of dielectric boundary points 3526 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2003 ## 204 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 8023 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.5510485E-08 3.7538491E-08 midg,1,midg; midg,igrid,midg -7.3691320E-09 3.5911231E-08 1,midg,midg; igrid,midg,midg -1.6626721E-09 4.3260549E-08 gauss-seidel spectral radius is 0.9879851 estimated iterations to convergence 74 setup time was (sec) 0.4800000 now iterating at: 23:14:09 rms-change max change #iterations 0.1580307 22.14073 at 10iterations 1.6668502E-02 2.756859 at 20iterations 1.7744068E-03 0.2709684 at 30iterations 2.9944736E-04 5.2754402E-02 at 40iterations 1.0874667E-04 2.0818233E-02 at 50iterations finished qdiffx linear iterations at : 23:14:11 total time elapsed so far: 2.910000 # loops : 50 mean,max change (kT/e) : 1.0874667E-04 2.0818233E-02 energy calculations done at 2.910000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.080000 DelPhi exited at 23:14:12 3.088u 0.134s 0:03.60 89.1% 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 23:14:12 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 = 2339 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: 1.971789 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): -11.81400 31.34100 ymin,ymax (A): -22.34300 31.82100 zmin,zma (A): -9.976000 43.33100 x,y,z range (A): 43.15500 54.16400 53.30700 scale (grids/A): 1.971789 object centre (A): 9.763500 4.739000 16.67750 number of atom coordinates read : 2339 total number of charged atoms : 2199 net assigned charge : 5.500004 assigned positive charge : 347.7804 centred at (gu) : 96.34691 91.33238 89.44013 assigned negative charge : -342.2808 centred at (gu) : 96.06334 90.95362 88.94126 start vw surface at 0.1500000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 74744 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20995 grid for indexing accessible points = 1.400000 m= 26436 mr = 51178 m= 4335 mr = 19299 m= 292 mr = 2779 m= 1 mr = 129 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5100000 number of dielectric boundary points 32423 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 113 iepsmp to db, and charging done at 0.6200000 number of grid points assigned charge 17334 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) : 0.6572631 object centre at (A) : 9.763500 4.739000 16.67750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.9911354E-02 1.1879511E-02 midg,1,midg; midg,igrid,midg 1.6864927E-02 2.7891040E-02 1,midg,midg; igrid,midg,midg -1.0206350E-02 9.1408566E-03 gauss-seidel spectral radius is 0.9987022 estimated iterations to convergence 220 setup time was (sec) 0.7800000 now iterating at: 23:14:13 rms-change max change #iterations 4.214123 169.4727 at 10iterations 2.014271 77.52341 at 20iterations 0.9634865 33.32792 at 30iterations 0.4595048 13.68455 at 40iterations 0.2188295 8.667269 at 50iterations 0.1050942 3.406652 at 60iterations 5.0016303E-02 1.826964 at 70iterations 2.3897270E-02 0.7127318 at 80iterations 1.1421652E-02 0.3439407 at 90iterations 5.4798429E-03 0.1942587 at 100iterations 2.6365237E-03 9.1003418E-02 at 110iterations 1.2837852E-03 4.3884277E-02 at 120iterations finished qdiffx linear iterations at : 23:14:19 total time elapsed so far: 7.170000 # loops : 120 mean,max change (kT/e) : 1.2837852E-03 4.3884277E-02 energy calculations done at 7.170000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.340000 DelPhi exited at 23:14:20 7.338u 0.173s 0:07.85 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 Sun Oct 9 2011 at 23:14:20 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2339 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: 2.957684 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): -11.81400 31.34100 ymin,ymax (A): -22.34300 31.82100 zmin,zma (A): -9.976000 43.33100 x,y,z range (A): 43.15500 54.16400 53.30700 scale (grids/A): 2.957684 object centre (A): 9.763500 4.739000 16.67750 number of atom coordinates read : 2339 total number of charged atoms : 2199 net assigned charge : 5.500004 assigned positive charge : 347.7804 centred at (gu) : 99.52034 91.99854 89.16013 assigned negative charge : -342.2808 centred at (gu) : 99.09501 91.43026 88.41187 start vw surface at 0.1300000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 172513 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20995 grid for indexing accessible points = 1.400000 m= 86152 mr = 124065 m= 30730 mr = 70099 m= 7969 mr = 24481 m= 1331 mr = 6074 m= 103 mr = 950 m= 2 mr = 58 m= 0 mr = 0 time to grow re-entrant surface = 0.7500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.280000 number of dielectric boundary points 73073 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.410000 number of grid points assigned charge 17591 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) : 1.971789 object centre at (A) : 9.763500 4.739000 16.67750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.4835356E-02 -3.5859607E-02 midg,1,midg; midg,igrid,midg 0.3372157 0.1323845 1,midg,midg; igrid,midg,midg -0.1783234 6.3618280E-02 gauss-seidel spectral radius is 0.9992766 estimated iterations to convergence 293 setup time was (sec) 1.570000 now iterating at: 23:14:21 rms-change max change #iterations 9.844533 308.9297 at 10iterations 5.807395 208.2658 at 20iterations 3.406026 97.68929 at 30iterations 1.995331 39.79854 at 40iterations 1.163889 24.93166 at 50iterations 0.6769654 14.31760 at 60iterations 0.3937291 7.513050 at 70iterations 0.2293296 4.322538 at 80iterations 0.1329400 2.449455 at 90iterations 7.7121519E-02 1.490535 at 100iterations 4.4774212E-02 0.8293724 at 110iterations 2.5949975E-02 0.5122890 at 120iterations 1.4995196E-02 0.2671424 at 130iterations 8.7039042E-03 0.1538258 at 140iterations 5.0458810E-03 8.8326931E-02 at 150iterations 2.9252330E-03 5.8329582E-02 at 160iterations 1.7017358E-03 3.0895233E-02 at 170iterations 9.9424762E-04 1.8312454E-02 at 180iterations finished qdiffx linear iterations at : 23:14:31 total time elapsed so far: 11.09000 # loops : 180 mean,max change (kT/e) : 9.9424762E-04 1.8312454E-02 energy calculations done at 11.09000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.27000 DelPhi exited at 23:14:32 11.269u 0.209s 0:11.92 96.1% 0+0k 0+0io 0pf+0w