Mon Oct 10 19:41:16 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 Mon Oct 10 2011 at 19:41:16 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4662 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1500000 grid size : 179 scale,in grids/A, set to be: 0.5112078 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): -18.52400 36.80000 ymin,ymax (A): -30.42400 31.50500 zmin,zma (A): -3.892000 65.74700 x,y,z range (A): 55.32401 61.92900 69.63900 scale (grids/A): 0.5112078 object centre (A): 9.138001 0.5404997 30.92750 number of atom coordinates read : 4662 total number of charged atoms : 4417 net assigned charge : 9.300048 assigned positive charge : 698.8126 centred at (gu) : 90.32571 90.82665 88.16958 assigned negative charge : -689.5170 centred at (gu) : 90.21284 90.90491 88.12417 start vw surface at 0.2300000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 7702 nv = 96 ne = 84 npr = 94037 no. pairs analyzed = 94037 no. exposed pairs = 6000 no. arc points = 41413 no. surface atoms = 2012 nbur = 2650 mkacc time = 0.2100000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.680000 m= 277 mr = 3955 m= 0 mr = 5 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4600000 number of dielectric boundary points 4019 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3949 ## 606 charges are in solution ## iepsmp to db, and charging done at 0.5700000 number of grid points assigned charge 10242 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.0547103E-11 1.5817643E-10 midg,1,midg; midg,igrid,midg 2.7103189E-10 -8.1361230E-11 1,midg,midg; igrid,midg,midg -1.4122124E-10 4.6054971E-10 gauss-seidel spectral radius is 0.9804236 estimated iterations to convergence 59 setup time was (sec) 0.6900000 now iterating at: 19:41:16 rms-change max change #iterations 6.7273244E-02 10.88843 at 10iterations 4.2619249E-03 0.6603870 at 20iterations 7.2432688E-04 9.7194433E-02 at 30iterations 2.6611343E-04 3.9206028E-02 at 40iterations 1.0545614E-04 1.5785694E-02 at 50iterations finished qdiffx linear iterations at : 19:41:19 total time elapsed so far: 3.170000 # loops : 50 mean,max change (kT/e) : 1.0545614E-04 1.5785694E-02 energy calculations done at 3.170000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.350000 DelPhi exited at 19:41:20 3.350u 0.144s 0:04.01 87.0% 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 Mon Oct 10 2011 at 19:41:20 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4662 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.533623 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): -18.52400 36.80000 ymin,ymax (A): -30.42400 31.50500 zmin,zma (A): -3.892000 65.74700 x,y,z range (A): 55.32401 61.92900 69.63900 scale (grids/A): 1.533623 object centre (A): 9.138001 0.5404997 30.92750 number of atom coordinates read : 4662 total number of charged atoms : 4417 net assigned charge : 9.300048 assigned positive charge : 698.8126 centred at (gu) : 90.97559 92.47868 84.50738 assigned negative charge : -689.5170 centred at (gu) : 90.63846 92.71457 84.37210 start vw surface at 0.1900000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 86678 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41413 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 25082 mr = 58956 m= 2255 mr = 16676 m= 47 mr = 962 m= 0 mr = 3 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 92 time to turn everything in is 0.5900000 number of dielectric boundary points 37465 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 574 ## 7 charges are in solution ## iepsmp to db, and charging done at 0.7100000 number of grid points assigned charge 33274 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) : 0.5112078 object centre at (A) : 9.138001 0.5404997 30.92750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.9544862E-03 2.0655995E-02 midg,1,midg; midg,igrid,midg 1.0278300E-02 -1.3133094E-02 1,midg,midg; igrid,midg,midg -8.7373820E-04 1.2962729E-02 gauss-seidel spectral radius is 0.9981077 estimated iterations to convergence 183 setup time was (sec) 0.8600000 now iterating at: 19:41:21 rms-change max change #iterations 3.768342 178.2062 at 10iterations 1.543244 57.01490 at 20iterations 0.6324983 23.34589 at 30iterations 0.2593664 8.133215 at 40iterations 0.1062575 3.587446 at 50iterations 4.3645728E-02 1.421194 at 60iterations 1.7949648E-02 0.5904676 at 70iterations 7.4273031E-03 0.2312832 at 80iterations 3.1214822E-03 0.1020002 at 90iterations 1.3524650E-03 5.8802605E-02 at 100iterations 6.3992676E-04 2.4213791E-02 at 110iterations 3.4761798E-04 1.2740135E-02 at 120iterations finished qdiffx linear iterations at : 19:41:27 total time elapsed so far: 7.290000 # loops : 120 mean,max change (kT/e) : 3.4761798E-04 1.2740135E-02 energy calculations done at 7.290000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.460000 DelPhi exited at 19:41:28 7.465u 0.176s 0:07.99 95.4% 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 Mon Oct 10 2011 at 19:41:28 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4662 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 2.300435 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): -18.52400 36.80000 ymin,ymax (A): -30.42400 31.50500 zmin,zma (A): -3.892000 65.74700 x,y,z range (A): 55.32401 61.92900 69.63900 scale (grids/A): 2.300435 object centre (A): 9.138001 0.5404997 30.92750 number of atom coordinates read : 4662 total number of charged atoms : 4417 net assigned charge : 9.300048 assigned positive charge : 698.8126 centred at (gu) : 91.46304 93.71763 81.76060 assigned negative charge : -689.5170 centred at (gu) : 90.95757 94.07182 81.55811 start vw surface at 0.2100000 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 201889 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41413 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 90131 mr = 145109 m= 22853 mr = 70224 m= 3238 mr = 16317 m= 164 mr = 1984 m= 1 mr = 58 m= 0 mr = 0 time to grow re-entrant surface = 0.8200000 no. cavity mid-points inaccessible to solvent = 327 time to turn everything in is 1.420000 number of dielectric boundary points 84584 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 73 iepsmp to db, and charging done at 1.550000 number of grid points assigned charge 35245 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) : 1.533623 object centre at (A) : 9.138001 0.5404997 30.92750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1591166 0.4707247 midg,1,midg; midg,igrid,midg 0.1407156 -0.2968284 1,midg,midg; igrid,midg,midg -1.3332322E-02 0.1857058 gauss-seidel spectral radius is 0.9991605 estimated iterations to convergence 273 setup time was (sec) 1.700000 now iterating at: 19:41:30 rms-change max change #iterations 10.12614 271.2390 at 10iterations 5.797633 124.5278 at 20iterations 3.294350 85.18860 at 30iterations 1.860896 41.81583 at 40iterations 1.050350 24.02317 at 50iterations 0.5889184 12.60977 at 60iterations 0.3305152 7.200211 at 70iterations 0.1846885 3.647579 at 80iterations 0.1031042 2.077085 at 90iterations 5.7381731E-02 1.178125 at 100iterations 3.2033019E-02 0.6615887 at 110iterations 1.7804360E-02 0.4101944 at 120iterations 9.8883789E-03 0.2050266 at 130iterations 5.5065104E-03 0.1074481 at 140iterations 3.0679388E-03 5.9038162E-02 at 150iterations 1.7049876E-03 3.9309502E-02 at 160iterations 9.5257506E-04 1.7291069E-02 at 170iterations 5.3506473E-04 1.0017395E-02 at 180iterations finished qdiffx linear iterations at : 19:41:39 total time elapsed so far: 11.56000 # loops : 180 mean,max change (kT/e) : 5.3506473E-04 1.0017395E-02 energy calculations done at 11.56000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.73000 DelPhi exited at 19:41:40 11.729u 0.166s 0:12.34 96.2% 0+0k 0+0io 0pf+0w