Wed Feb 15 08:55:37 PST 2012 #!/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_thinner.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 Feb 15 2012 at 08:55:37 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 = 2208 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: 0.6945393 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): 35.28000 80.20100 ymin,ymax (A): 30.10900 77.33300 zmin,zma (A): 1.519000 52.77600 x,y,z range (A): 44.92100 47.22400 51.25700 scale (grids/A): 0.6945393 object centre (A): 57.74050 53.72100 27.14750 number of atom coordinates read : 2208 total number of charged atoms : 2070 net assigned charge : 2.500009 assigned positive charge : 326.0924 centred at (gu) : 89.51273 89.30074 88.97253 assigned negative charge : -323.5929 centred at (gu) : 89.44853 89.34455 88.79568 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7065 nv = 96 ne = 84 npr = 47010 no. pairs analyzed = 47010 no. exposed pairs = 2786 no. arc points = 19579 no. surface atoms = 927 nbur = 1281 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 438 mr = 3833 m= 4 mr = 57 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 15 time to turn everything in is 0.2900000 number of dielectric boundary points 3617 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1770 ## 139 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 8030 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.4968269E-08 6.7325836E-08 midg,1,midg; midg,igrid,midg 3.7854484E-08 -3.2407307E-10 1,midg,midg; igrid,midg,midg -9.3444816E-09 3.6914908E-08 gauss-seidel spectral radius is 0.9892150 estimated iterations to convergence 78 setup time was (sec) 0.5300000 now iterating at: 08:55:38 rms-change max change #iterations 0.1828274 24.11966 at 10iterations 2.1479940E-02 2.839157 at 20iterations 2.6161317E-03 0.3651772 at 30iterations 3.5404266E-04 4.6415329E-02 at 40iterations 6.2237203E-05 1.0013580E-02 at 50iterations finished qdiffx linear iterations at : 08:55:41 total time elapsed so far: 3.290000 # loops : 50 mean,max change (kT/e) : 6.2237203E-05 1.0013580E-02 energy calculations done at 3.290000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.490000 DelPhi exited at 08:55:41 3.495u 0.171s 0:04.03 90.8% 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 Feb 15 2012 at 08:55:41 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 = 2208 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: 2.083618 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): 35.28000 80.20100 ymin,ymax (A): 30.10900 77.33300 zmin,zma (A): 1.519000 52.77600 x,y,z range (A): 44.92100 47.22400 51.25700 scale (grids/A): 2.083618 object centre (A): 57.74050 53.72100 27.14750 number of atom coordinates read : 2208 total number of charged atoms : 2070 net assigned charge : 2.500009 assigned positive charge : 326.0924 centred at (gu) : 88.53795 87.90216 86.91708 assigned negative charge : -323.5929 centred at (gu) : 88.34563 88.03368 86.38703 start vw surface at 0.1300000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 75846 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19579 grid for indexing accessible points = 1.400000 m= 28216 mr = 52188 m= 5407 mr = 20717 m= 459 mr = 3375 m= 13 mr = 161 m= 1 mr = 1 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 371 time to turn everything in is 0.5700000 number of dielectric boundary points 33500 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 91 iepsmp to db, and charging done at 0.6900000 number of grid points assigned charge 16436 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) : 0.6945393 object centre at (A) : 57.74050 53.72100 27.14750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.5840102E-02 5.9492145E-02 midg,1,midg; midg,igrid,midg -3.5844501E-02 -2.5600722E-02 1,midg,midg; igrid,midg,midg -1.3481093E-02 1.6572949E-02 gauss-seidel spectral radius is 0.9988119 estimated iterations to convergence 230 setup time was (sec) 0.8600000 now iterating at: 08:55:42 rms-change max change #iterations 4.577448 187.0781 at 10iterations 2.243702 76.73476 at 20iterations 1.111074 33.64938 at 30iterations 0.5489017 17.49000 at 40iterations 0.2705928 8.206062 at 50iterations 0.1331998 4.412971 at 60iterations 6.5730222E-02 2.071861 at 70iterations 3.2494724E-02 0.9872446 at 80iterations 1.5996268E-02 0.5082059 at 90iterations 7.9283165E-03 0.2272816 at 100iterations 3.9084530E-03 0.1231689 at 110iterations 1.9272815E-03 5.7956696E-02 at 120iterations finished qdiffx linear iterations at : 08:55:50 total time elapsed so far: 8.840000 # loops : 120 mean,max change (kT/e) : 1.9272815E-03 5.7956696E-02 energy calculations done at 8.840000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.040000 DelPhi exited at 08:55:51 9.039u 0.207s 0:09.88 93.4% 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 Feb 15 2012 at 08:55:51 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2208 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: 3.125427 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): 35.28000 80.20100 ymin,ymax (A): 30.10900 77.33300 zmin,zma (A): 1.519000 52.77600 x,y,z range (A): 44.92100 47.22400 51.25700 scale (grids/A): 3.125427 object centre (A): 57.74050 53.72100 27.14750 number of atom coordinates read : 2208 total number of charged atoms : 2070 net assigned charge : 2.500009 assigned positive charge : 326.0924 centred at (gu) : 87.80685 86.85308 85.37556 assigned negative charge : -323.5929 centred at (gu) : 87.51841 87.05054 84.58056 start vw surface at 0.1600000 fill in re-entrant regions at 0.9000000 boundary points on vw surface= 175552 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19579 grid for indexing accessible points = 1.400000 m= 88149 mr = 126518 m= 35297 mr = 71901 m= 9997 mr = 28277 m= 1825 mr = 7397 m= 183 mr = 1183 m= 6 mr = 80 m= 0 mr = 0 time to grow re-entrant surface = 0.9200000 no. cavity mid-points inaccessible to solvent = 1339 time to turn everything in is 1.960000 number of dielectric boundary points 75653 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.110000 number of grid points assigned charge 16560 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) : 2.083618 object centre at (A) : 57.74050 53.72100 27.14750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.4807525 0.3841088 midg,1,midg; midg,igrid,midg -0.4631811 -0.2396713 1,midg,midg; igrid,midg,midg -0.1744225 0.1203125 gauss-seidel spectral radius is 0.9993053 estimated iterations to convergence 299 setup time was (sec) 2.290000 now iterating at: 08:55:54 rms-change max change #iterations 10.32922 355.9846 at 10iterations 6.087115 124.9474 at 20iterations 3.598191 74.62778 at 30iterations 2.115319 44.94974 at 40iterations 1.244935 23.08662 at 50iterations 0.7295574 13.10000 at 60iterations 0.4281753 7.648834 at 70iterations 0.2509602 4.478354 at 80iterations 0.1467546 2.611850 at 90iterations 8.5990071E-02 1.589722 at 100iterations 5.0343528E-02 0.8620853 at 110iterations 2.9380100E-02 0.4750844 at 120iterations 1.7179640E-02 0.3072104 at 130iterations 1.0068383E-02 0.1932182 at 140iterations 5.8970298E-03 0.1074040 at 150iterations 3.4461715E-03 6.2215328E-02 at 160iterations 2.0170610E-03 3.4750342E-02 at 170iterations 1.1915440E-03 2.0317078E-02 at 180iterations finished qdiffx linear iterations at : 08:56:04 total time elapsed so far: 12.93000 # loops : 180 mean,max change (kT/e) : 1.1915440E-03 2.0317078E-02 energy calculations done at 12.93000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.12000 DelPhi exited at 08:56:06 13.122u 0.244s 0:15.17 88.0% 0+0k 0+0io 0pf+0w