Wed Dec 28 11:02:00 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+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 Wed Dec 28 2011 at 11:02:01 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: 247 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1966 !!! WARNING: ASH 25 has a net charge of -0.3190 !!! WARNING: ASH 125 has a net charge of -0.3190 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: 0.6491494 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): -6.225000 34.29100 ymin,ymax (A): -3.427000 49.34200 zmin,zma (A): -23.96500 30.87600 x,y,z range (A): 40.51600 52.76900 54.84100 scale (grids/A): 0.6491494 object centre (A): 14.03300 22.95750 3.455500 number of atom coordinates read : 1966 total number of charged atoms : 1832 net assigned charge : 3.362005 assigned positive charge : 287.8021 centred at (gu) : 90.93060 92.23851 90.15686 assigned negative charge : -284.4403 centred at (gu) : 91.07204 92.39307 90.08040 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 5688 nv = 96 ne = 84 npr = 40226 no. pairs analyzed = 40226 no. exposed pairs = 2462 no. arc points = 17472 no. surface atoms = 835 nbur = 1131 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 276 mr = 3139 m= 1 mr = 37 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 2789 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1757 ## 172 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 6598 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.4027096E-09 1.5635546E-08 midg,1,midg; midg,igrid,midg 1.4641676E-08 -1.6844380E-08 1,midg,midg; igrid,midg,midg 1.8092051E-08 -1.0707999E-08 gauss-seidel spectral radius is 0.9876476 estimated iterations to convergence 74 setup time was (sec) 0.6000000 now iterating at: 11:02:02 rms-change max change #iterations 0.1294113 23.69577 at 10iterations 1.2980120E-02 2.200732 at 20iterations 1.3557206E-03 0.2576087 at 30iterations 1.3723770E-04 1.9659042E-02 at 40iterations 1.3830456E-05 2.4261475E-03 at 50iterations finished qdiffx linear iterations at : 11:02:05 total time elapsed so far: 4.280000 # loops : 50 mean,max change (kT/e) : 1.3830456E-05 2.4261475E-03 energy calculations done at 4.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.490000 DelPhi exited at 11:02:08 4.495u 0.446s 0:07.07 69.7% 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 Wed Dec 28 2011 at 11:02:08 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: 247 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1966 !!! WARNING: ASH 25 has a net charge of -0.3190 !!! WARNING: ASH 125 has a net charge of -0.3190 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: 1.947448 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): -6.225000 34.29100 ymin,ymax (A): -3.427000 49.34200 zmin,zma (A): -23.96500 30.87600 x,y,z range (A): 40.51600 52.76900 54.84100 scale (grids/A): 1.947448 object centre (A): 14.03300 22.95750 3.455500 number of atom coordinates read : 1966 total number of charged atoms : 1832 net assigned charge : 3.362005 assigned positive charge : 287.8021 centred at (gu) : 92.79173 96.71567 90.47078 assigned negative charge : -284.4403 centred at (gu) : 93.21624 97.17940 90.24146 start vw surface at 0.1200000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 60993 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17472 grid for indexing accessible points = 1.400000 m= 22272 mr = 41925 m= 3530 mr = 17013 m= 201 mr = 2376 m= 1 mr = 90 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 2900 time to turn everything in is 0.6200000 number of dielectric boundary points 25593 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 140 iepsmp to db, and charging done at 0.7500000 number of grid points assigned charge 14454 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) : 0.6491494 object centre at (A) : 14.03300 22.95750 3.455500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.2980567E-02 1.9076457E-02 midg,1,midg; midg,igrid,midg 3.4833927E-02 -1.2855691E-02 1,midg,midg; igrid,midg,midg 8.4507503E-03 -4.4042240E-03 gauss-seidel spectral radius is 0.9986170 estimated iterations to convergence 213 setup time was (sec) 0.9500000 now iterating at: 11:02:09 rms-change max change #iterations 3.706537 203.4365 at 10iterations 1.727200 63.56776 at 20iterations 0.8040601 29.17643 at 30iterations 0.3757195 13.17741 at 40iterations 0.1736002 6.143051 at 50iterations 8.0918439E-02 2.758060 at 60iterations 3.7899543E-02 1.337711 at 70iterations 1.7592095E-02 0.6296120 at 80iterations 8.1824949E-03 0.2729070 at 90iterations 3.8164353E-03 0.1380816 at 100iterations 1.7733532E-03 5.9581757E-02 at 110iterations 8.2838163E-04 2.8030396E-02 at 120iterations finished qdiffx linear iterations at : 11:02:18 total time elapsed so far: 10.07000 # loops : 120 mean,max change (kT/e) : 8.2838163E-04 2.8030396E-02 energy calculations done at 10.07000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.28000 DelPhi exited at 11:02:20 10.287u 0.487s 0:11.89 90.4% 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 Wed Dec 28 2011 at 11:02:20 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: 247 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1966 !!! WARNING: ASH 25 has a net charge of -0.3190 !!! WARNING: ASH 125 has a net charge of -0.3190 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: 2.921172 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): -6.225000 34.29100 ymin,ymax (A): -3.427000 49.34200 zmin,zma (A): -23.96500 30.87600 x,y,z range (A): 40.51600 52.76900 54.84100 scale (grids/A): 2.921172 object centre (A): 14.03300 22.95750 3.455500 number of atom coordinates read : 1966 total number of charged atoms : 1832 net assigned charge : 3.362005 assigned positive charge : 287.8021 centred at (gu) : 94.18771 100.0737 90.70597 assigned negative charge : -284.4403 centred at (gu) : 94.82452 100.7692 90.36222 start vw surface at 0.1400000 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 140737 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17472 grid for indexing accessible points = 1.400000 m= 71608 mr = 101255 m= 26772 mr = 59516 m= 6328 mr = 22183 m= 884 mr = 5023 m= 38 mr = 676 m= 0 mr = 20 time to grow re-entrant surface = 0.9600000 no. cavity mid-points inaccessible to solvent = 9424 time to turn everything in is 1.630000 number of dielectric boundary points 57694 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.780000 number of grid points assigned charge 14656 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) : 1.947448 object centre at (A) : 14.03300 22.95750 3.455500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.010919 5.2829791E-02 midg,1,midg; midg,igrid,midg 0.3247279 -0.1555266 1,midg,midg; igrid,midg,midg 4.8753705E-02 -1.6435152E-02 gauss-seidel spectral radius is 0.9992406 estimated iterations to convergence 286 setup time was (sec) 1.980000 now iterating at: 11:02:22 rms-change max change #iterations 8.613878 458.4994 at 10iterations 4.923972 124.5363 at 20iterations 2.804484 61.92722 at 30iterations 1.597671 35.06579 at 40iterations 0.9120152 18.63507 at 50iterations 0.5200465 10.00321 at 60iterations 0.2961178 6.340191 at 70iterations 0.1677861 3.365913 at 80iterations 9.5712744E-02 1.885445 at 90iterations 5.4618247E-02 1.077161 at 100iterations 3.1012705E-02 0.5874035 at 110iterations 1.7638734E-02 0.3337555 at 120iterations 1.0030579E-02 0.2320919 at 130iterations 5.7058479E-03 0.1336517 at 140iterations 3.2512627E-03 6.2359333E-02 at 150iterations 1.8499701E-03 3.6878109E-02 at 160iterations 1.0555569E-03 2.1661520E-02 at 170iterations 6.0053763E-04 1.2055397E-02 at 180iterations finished qdiffx linear iterations at : 11:02:37 total time elapsed so far: 16.86000 # loops : 180 mean,max change (kT/e) : 6.0053763E-04 1.2055397E-02 energy calculations done at 16.86000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.08000 DelPhi exited at 11:02:38 17.082u 0.490s 0:18.38 95.5% 0+0k 0+0io 0pf+0w