Sat Oct 8 11:48:56 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 Sat Oct 8 2011 at 11:48:56 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: 308 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3116 !!! WARNING: HIT 138 has a net charge of 0.5140 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: 0.5765556 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): -12.75000 43.46400 ymin,ymax (A): -8.610001 53.13600 zmin,zma (A): 17.65300 73.05400 x,y,z range (A): 56.21400 61.74600 55.40100 scale (grids/A): 0.5765556 object centre (A): 15.35700 22.26300 45.35350 number of atom coordinates read : 3116 total number of charged atoms : 2958 net assigned charge : -7.485989 assigned positive charge : 464.8275 centred at (gu) : 90.69891 91.99246 91.54604 assigned negative charge : -472.3148 centred at (gu) : 90.74230 91.97881 91.44550 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6856 nv = 96 ne = 84 npr = 61264 no. pairs analyzed = 61264 no. exposed pairs = 4365 no. arc points = 31607 no. surface atoms = 1435 nbur = 1681 mkacc time = 0.1100000 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 = 1.484000 m= 288 mr = 3254 m= 2 mr = 15 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 0.2200000 number of dielectric boundary points 3877 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3125 ## 353 charges are in solution ## iepsmp to db, and charging done at 0.2900000 number of grid points assigned charge 8770 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.4965641E-09 8.8478458E-10 midg,1,midg; midg,igrid,midg -1.1162185E-09 -1.8755046E-09 1,midg,midg; igrid,midg,midg -5.0053978E-10 -2.7962812E-09 gauss-seidel spectral radius is 0.9844980 estimated iterations to convergence 66 setup time was (sec) 0.4100000 now iterating at: 11:48:56 rms-change max change #iterations 9.6477121E-02 14.14400 at 10iterations 7.6146061E-03 1.080322 at 20iterations 5.9109379E-04 8.9618683E-02 at 30iterations 4.8592781E-05 7.8582764E-03 at 40iterations 5.5617497E-06 7.2479248E-04 at 50iterations finished qdiffx linear iterations at : 11:49:01 total time elapsed so far: 3.300000 # loops : 50 mean,max change (kT/e) : 5.5617497E-06 7.2479248E-04 energy calculations done at 3.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.430000 DelPhi exited at 11:49:02 3.432u 0.174s 0:05.82 61.8% 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 Sat Oct 8 2011 at 11:49:02 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: 308 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3116 !!! WARNING: HIT 138 has a net charge of 0.5140 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: 1.729667 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): -12.75000 43.46400 ymin,ymax (A): -8.610001 53.13600 zmin,zma (A): 17.65300 73.05400 x,y,z range (A): 56.21400 61.74600 55.40100 scale (grids/A): 1.729667 object centre (A): 15.35700 22.26300 45.35350 number of atom coordinates read : 3116 total number of charged atoms : 2958 net assigned charge : -7.485989 assigned positive charge : 464.8275 centred at (gu) : 92.09589 95.97650 94.63681 assigned negative charge : -472.3148 centred at (gu) : 92.22678 95.93591 94.33618 start vw surface at 0.1000000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 74828 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31607 grid for indexing accessible points = 1.400000 m= 22434 mr = 48059 m= 2604 mr = 14514 m= 107 mr = 1276 m= 1 mr = 13 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 36112 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 301 iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 22950 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) : 0.5765556 object centre at (A) : 15.35700 22.26300 45.35350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.4397433E-03 8.7849889E-03 midg,1,midg; midg,igrid,midg -2.6486784E-02 -1.0552460E-02 1,midg,midg; igrid,midg,midg -1.9970017E-03 -1.5601156E-02 gauss-seidel spectral radius is 0.9984207 estimated iterations to convergence 200 setup time was (sec) 0.5700000 now iterating at: 11:49:02 rms-change max change #iterations 3.889894 196.1602 at 10iterations 1.706888 65.76633 at 20iterations 0.7503197 24.75787 at 30iterations 0.3306774 11.56379 at 40iterations 0.1455356 5.721142 at 50iterations 6.4200275E-02 2.213731 at 60iterations 2.8336963E-02 1.028156 at 70iterations 1.2513748E-02 0.4094425 at 80iterations 5.4965704E-03 0.1914234 at 90iterations 2.4299971E-03 8.2942963E-02 at 100iterations 1.0763252E-03 3.5037994E-02 at 110iterations 4.7637508E-04 1.6156197E-02 at 120iterations finished qdiffx linear iterations at : 11:49:12 total time elapsed so far: 7.680000 # loops : 120 mean,max change (kT/e) : 4.7637508E-04 1.6156197E-02 energy calculations done at 7.680000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.810000 DelPhi exited at 11:49:13 7.817u 0.202s 0:10.93 73.2% 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 Sat Oct 8 2011 at 11:49:13 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: 308 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3116 !!! WARNING: HIT 138 has a net charge of 0.5140 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: 2.594500 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): -12.75000 43.46400 ymin,ymax (A): -8.610001 53.13600 zmin,zma (A): 17.65300 73.05400 x,y,z range (A): 56.21400 61.74600 55.40100 scale (grids/A): 2.594500 object centre (A): 15.35700 22.26300 45.35350 number of atom coordinates read : 3116 total number of charged atoms : 2958 net assigned charge : -7.485989 assigned positive charge : 464.8275 centred at (gu) : 93.14346 98.96441 96.95515 assigned negative charge : -472.3148 centred at (gu) : 93.33992 98.90376 96.50417 start vw surface at 0.1100000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 173517 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31607 grid for indexing accessible points = 1.400000 m= 76254 mr = 118318 m= 22537 mr = 57954 m= 4161 mr = 16384 m= 379 mr = 2599 m= 10 mr = 183 m= 0 mr = 0 time to grow re-entrant surface = 0.5000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.9100000 number of dielectric boundary points 81420 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 15 iepsmp to db, and charging done at 1.010000 number of grid points assigned charge 23650 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) : 1.729667 object centre at (A) : 15.35700 22.26300 45.35350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1311709 0.1703895 midg,1,midg; midg,igrid,midg -0.1850221 -0.1769454 1,midg,midg; igrid,midg,midg 4.9489841E-02 -0.2035231 gauss-seidel spectral radius is 0.9992244 estimated iterations to convergence 283 setup time was (sec) 1.160000 now iterating at: 11:49:14 rms-change max change #iterations 9.824087 336.2500 at 10iterations 5.706395 143.4673 at 20iterations 3.284619 73.16109 at 30iterations 1.891366 37.05150 at 40iterations 1.081443 24.14878 at 50iterations 0.6185122 13.52495 at 60iterations 0.3525557 7.229633 at 70iterations 0.2007817 4.029770 at 80iterations 0.1142870 2.202273 at 90iterations 6.5049022E-02 1.391872 at 100iterations 3.6902323E-02 0.7455863 at 110iterations 2.0980133E-02 0.4481850 at 120iterations 1.1896859E-02 0.2252808 at 130iterations 6.7479657E-03 0.1335382 at 140iterations 3.8237551E-03 8.1009865E-02 at 150iterations 2.1673499E-03 4.3147087E-02 at 160iterations 1.2278142E-03 2.5726318E-02 at 170iterations 6.9694524E-04 1.3617516E-02 at 180iterations finished qdiffx linear iterations at : 11:49:26 total time elapsed so far: 13.17000 # loops : 180 mean,max change (kT/e) : 6.9694524E-04 1.3617516E-02 energy calculations done at 13.17000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.30000 DelPhi exited at 11:49:27 13.299u 0.220s 0:13.84 97.6% 0+0k 0+0io 0pf+0w