Sun Oct 9 12:42:54 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+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 Sun Oct 9 2011 at 12:42:55 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: 301 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2442 !!! WARNING: GLM 273 has a net charge of -0.0940 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: 0.6993420 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): -9.948000 35.99500 ymin,ymax (A): -4.009000 46.89600 zmin,zma (A): -7.127000 37.74700 x,y,z range (A): 45.94300 50.90500 44.87400 scale (grids/A): 0.6993420 object centre (A): 13.02350 21.44350 15.31000 number of atom coordinates read : 2442 total number of charged atoms : 2296 net assigned charge : 5.406007 assigned positive charge : 376.4298 centred at (gu) : 90.41196 90.33414 89.74879 assigned negative charge : -371.0244 centred at (gu) : 90.51710 90.19759 89.68270 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7785 nv = 96 ne = 84 npr = 50177 no. pairs analyzed = 50177 no. exposed pairs = 2926 no. arc points = 20253 no. surface atoms = 992 nbur = 1450 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 466 mr = 4393 m= 0 mr = 73 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 22 time to turn everything in is 0.1900000 number of dielectric boundary points 3785 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1865 ## 171 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 8996 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.3073257E-09 6.6571872E-08 midg,1,midg; midg,igrid,midg -2.7970970E-08 1.1082196E-07 1,midg,midg; igrid,midg,midg 8.1823501E-08 -1.5747721E-08 gauss-seidel spectral radius is 0.9893755 estimated iterations to convergence 79 setup time was (sec) 0.3700000 now iterating at: 12:42:55 rms-change max change #iterations 0.2152093 28.76469 at 10iterations 2.6162105E-02 3.902967 at 20iterations 3.3304053E-03 0.3903923 at 30iterations 4.6860220E-04 5.9852600E-02 at 40iterations 8.9360816E-05 1.2165070E-02 at 50iterations finished qdiffx linear iterations at : 12:42:58 total time elapsed so far: 3.220000 # loops : 50 mean,max change (kT/e) : 8.9360816E-05 1.2165070E-02 energy calculations done at 3.220000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.350000 DelPhi exited at 12:42:58 3.350u 0.191s 0:03.81 92.9% 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 12:42:58 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: 301 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2442 !!! WARNING: GLM 273 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.098026 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): -9.948000 35.99500 ymin,ymax (A): -4.009000 46.89600 zmin,zma (A): -7.127000 37.74700 x,y,z range (A): 45.94300 50.90500 44.87400 scale (grids/A): 2.098026 object centre (A): 13.02350 21.44350 15.31000 number of atom coordinates read : 2442 total number of charged atoms : 2296 net assigned charge : 5.406007 assigned positive charge : 376.4298 centred at (gu) : 91.23521 91.00217 89.24599 assigned negative charge : -371.0244 centred at (gu) : 91.55099 90.59230 89.04773 start vw surface at 0.1000000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 83384 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20253 grid for indexing accessible points = 1.400000 m= 31285 mr = 58760 m= 5454 mr = 23350 m= 452 mr = 3494 m= 11 mr = 241 m= 0 mr = 2 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 350 time to turn everything in is 0.4200000 number of dielectric boundary points 34739 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 90 iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 18227 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) : 0.6993420 object centre at (A) : 13.02350 21.44350 15.31000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.6743515E-02 5.6233428E-02 midg,1,midg; midg,igrid,midg -3.1802788E-02 3.5758916E-02 1,midg,midg; igrid,midg,midg 6.9517829E-04 1.4185394E-03 gauss-seidel spectral radius is 0.9988408 estimated iterations to convergence 232 setup time was (sec) 0.6400000 now iterating at: 12:42:59 rms-change max change #iterations 5.035537 214.4451 at 10iterations 2.497406 89.43875 at 20iterations 1.236323 39.45073 at 30iterations 0.6165930 17.57412 at 40iterations 0.3076201 8.888985 at 50iterations 0.1528623 4.599084 at 60iterations 7.6136120E-02 2.208205 at 70iterations 3.8003944E-02 1.141120 at 80iterations 1.8949449E-02 0.4924622 at 90iterations 9.4595496E-03 0.2796152 at 100iterations 4.7309059E-03 0.1462936 at 110iterations 2.3683566E-03 6.3069820E-02 at 120iterations finished qdiffx linear iterations at : 12:43:06 total time elapsed so far: 7.690000 # loops : 120 mean,max change (kT/e) : 2.3683566E-03 6.3069820E-02 energy calculations done at 7.690000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.810000 DelPhi exited at 12:43:07 7.817u 0.184s 0:08.27 96.6% 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 12:43:07 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: 301 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2442 !!! WARNING: GLM 273 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.147039 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): -9.948000 35.99500 ymin,ymax (A): -4.009000 46.89600 zmin,zma (A): -7.127000 37.74700 x,y,z range (A): 45.94300 50.90500 44.87400 scale (grids/A): 3.147039 object centre (A): 13.02350 21.44350 15.31000 number of atom coordinates read : 2442 total number of charged atoms : 2296 net assigned charge : 5.406007 assigned positive charge : 376.4298 centred at (gu) : 91.85267 91.50309 88.86874 assigned negative charge : -371.0244 centred at (gu) : 92.32635 90.88837 88.57148 start vw surface at 0.1000000 fill in re-entrant regions at 0.5600000 boundary points on vw surface= 192224 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20253 grid for indexing accessible points = 1.400000 m= 99709 mr = 141534 m= 38162 mr = 82471 m= 10218 mr = 30899 m= 1928 mr = 7820 m= 193 mr = 1396 m= 7 mr = 116 m= 0 mr = 0 time to grow re-entrant surface = 0.6300000 no. cavity mid-points inaccessible to solvent = 1139 time to turn everything in is 1.270000 number of dielectric boundary points 78205 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.370000 number of grid points assigned charge 18368 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) : 2.098026 object centre at (A) : 13.02350 21.44350 15.31000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.0253457E-02 0.4515373 midg,1,midg; midg,igrid,midg -0.2859878 0.2300152 1,midg,midg; igrid,midg,midg -9.7336963E-02 1.3524293E-02 gauss-seidel spectral radius is 0.9993009 estimated iterations to convergence 298 setup time was (sec) 1.500000 now iterating at: 12:43:08 rms-change max change #iterations 11.19461 372.6534 at 10iterations 6.637704 126.3665 at 20iterations 3.927013 68.16537 at 30iterations 2.322571 40.15498 at 40iterations 1.367879 23.94885 at 50iterations 0.8028865 15.13455 at 60iterations 0.4720805 7.977665 at 70iterations 0.2771329 4.442641 at 80iterations 0.1626966 2.786636 at 90iterations 9.5474891E-02 1.628336 at 100iterations 5.5965740E-02 0.9160078 at 110iterations 3.2834072E-02 0.5281372 at 120iterations 1.9368974E-02 0.3234320 at 130iterations 1.1428866E-02 0.2025375 at 140iterations 6.8294886E-03 0.1211281 at 150iterations 4.1294862E-03 7.9437256E-02 at 160iterations 2.5624954E-03 4.8416138E-02 at 170iterations 1.6419883E-03 3.3729553E-02 at 180iterations finished qdiffx linear iterations at : 12:43:20 total time elapsed so far: 12.82000 # loops : 180 mean,max change (kT/e) : 1.6419883E-03 3.3729553E-02 energy calculations done at 12.82000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.95000 DelPhi exited at 12:43:20 12.953u 0.204s 0:13.44 97.8% 0+0k 0+0io 0pf+0w