Sat Oct 8 15:11:20 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 15:11:20 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2431 !!! WARNING: GLM 258 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.5963948 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): 13.10300 72.79500 ymin,ymax (A): -13.31000 32.73600 zmin,zma (A): -3.179000 51.67100 x,y,z range (A): 59.69200 46.04600 54.85000 scale (grids/A): 0.5963948 object centre (A): 42.94900 9.712999 24.24600 number of atom coordinates read : 2431 total number of charged atoms : 2351 net assigned charge : 8.406016 assigned positive charge : 369.6071 centred at (gu) : 90.53165 89.09151 90.36378 assigned negative charge : -361.2017 centred at (gu) : 90.44024 89.00193 90.52225 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6016 nv = 96 ne = 84 npr = 45536 no. pairs analyzed = 45536 no. exposed pairs = 3421 no. arc points = 24693 no. surface atoms = 1141 nbur = 1290 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 279 mr = 2953 m= 1 mr = 13 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 0.3500000 number of dielectric boundary points 3330 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2462 ## 254 charges are in solution ## iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 7457 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.3217481E-09 -1.8221594E-09 midg,1,midg; midg,igrid,midg 5.6327187E-10 4.8284967E-09 1,midg,midg; igrid,midg,midg 4.0128581E-10 6.7436279E-09 gauss-seidel spectral radius is 0.9854484 estimated iterations to convergence 68 setup time was (sec) 0.6900000 now iterating at: 15:11:21 rms-change max change #iterations 0.1033769 17.49116 at 10iterations 8.6643444E-03 1.427940 at 20iterations 7.6023873E-04 0.1199150 at 30iterations 7.6314398E-05 1.1522293E-02 at 40iterations 1.1296570E-05 1.6193390E-03 at 50iterations finished qdiffx linear iterations at : 15:11:24 total time elapsed so far: 4.200000 # loops : 50 mean,max change (kT/e) : 1.1296570E-05 1.6193390E-03 energy calculations done at 4.200000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.410000 DelPhi exited at 15:11:25 4.412u 0.427s 0:05.14 93.9% 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 Sat Oct 8 2011 at 15:11:25 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2431 !!! WARNING: GLM 258 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.789185 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): 13.10300 72.79500 ymin,ymax (A): -13.31000 32.73600 zmin,zma (A): -3.179000 51.67100 x,y,z range (A): 59.69200 46.04600 54.85000 scale (grids/A): 1.789185 object centre (A): 42.94900 9.712999 24.24600 number of atom coordinates read : 2431 total number of charged atoms : 2351 net assigned charge : 8.406016 assigned positive charge : 369.6071 centred at (gu) : 91.59450 87.27405 91.09100 assigned negative charge : -361.2017 centred at (gu) : 91.32068 87.00576 91.56664 start vw surface at 0.1400000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 64974 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24693 grid for indexing accessible points = 1.400000 m= 21005 mr = 42518 m= 2669 mr = 14133 m= 102 mr = 1344 m= 0 mr = 12 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6600000 number of dielectric boundary points 30743 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 216 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.8500000 number of grid points assigned charge 18317 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) : 0.5963948 object centre at (A) : 42.94900 9.712999 24.24600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.0048138E-02 -5.9677516E-03 midg,1,midg; midg,igrid,midg 1.0351958E-02 9.4619887E-03 1,midg,midg; igrid,midg,midg 2.7747342E-02 4.9872525E-02 gauss-seidel spectral radius is 0.9984512 estimated iterations to convergence 202 setup time was (sec) 1.050000 now iterating at: 15:11:26 rms-change max change #iterations 3.577385 192.2637 at 10iterations 1.591834 58.08169 at 20iterations 0.7057644 26.50382 at 30iterations 0.3124654 10.60340 at 40iterations 0.1386843 5.591016 at 50iterations 6.1811548E-02 2.151114 at 60iterations 2.7351908E-02 1.032642 at 70iterations 1.2265479E-02 0.4197845 at 80iterations 5.4494622E-03 0.1911724 at 90iterations 2.4305566E-03 9.1033936E-02 at 100iterations 1.0904728E-03 4.2478085E-02 at 110iterations 4.8617023E-04 1.8167496E-02 at 120iterations finished qdiffx linear iterations at : 15:11:35 total time elapsed so far: 9.920000 # loops : 120 mean,max change (kT/e) : 4.8617023E-04 1.8167496E-02 energy calculations done at 9.920000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.13000 DelPhi exited at 15:11:36 10.139u 0.463s 0:10.92 96.9% 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 Sat Oct 8 2011 at 15:11:36 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2431 !!! WARNING: GLM 258 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.683777 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): 13.10300 72.79500 ymin,ymax (A): -13.31000 32.73600 zmin,zma (A): -3.179000 51.67100 x,y,z range (A): 59.69200 46.04600 54.85000 scale (grids/A): 2.683777 object centre (A): 42.94900 9.712999 24.24600 number of atom coordinates read : 2431 total number of charged atoms : 2351 net assigned charge : 8.406016 assigned positive charge : 369.6071 centred at (gu) : 92.39153 85.91099 91.63631 assigned negative charge : -361.2017 centred at (gu) : 91.98090 85.50864 92.34988 start vw surface at 0.1700000 fill in re-entrant regions at 0.5600000 boundary points on vw surface= 150266 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24693 grid for indexing accessible points = 1.400000 m= 70282 mr = 104063 m= 22322 mr = 54470 m= 4396 mr = 16557 m= 416 mr = 2943 m= 11 mr = 188 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 1.020000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.690000 number of dielectric boundary points 69473 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 1.850000 number of grid points assigned charge 18802 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) : 1.789185 object centre at (A) : 42.94900 9.712999 24.24600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.4619888E-02 -3.2323077E-02 midg,1,midg; midg,igrid,midg 0.1344876 8.0976032E-02 1,midg,midg; igrid,midg,midg 0.5304608 1.013823 gauss-seidel spectral radius is 0.9992224 estimated iterations to convergence 283 setup time was (sec) 2.080000 now iterating at: 15:11:38 rms-change max change #iterations 8.966742 273.2198 at 10iterations 5.273412 144.4054 at 20iterations 3.064698 81.69354 at 30iterations 1.769632 43.49600 at 40iterations 1.015023 23.37871 at 50iterations 0.5820619 11.27028 at 60iterations 0.3330472 8.095673 at 70iterations 0.1892639 3.798555 at 80iterations 0.1077305 2.147718 at 90iterations 6.1391365E-02 1.465636 at 100iterations 3.4877483E-02 0.6956253 at 110iterations 1.9820016E-02 0.4197088 at 120iterations 1.1215067E-02 0.2347140 at 130iterations 6.3749310E-03 0.1308041 at 140iterations 3.6189123E-03 7.7247620E-02 at 150iterations 2.0489460E-03 4.2210579E-02 at 160iterations 1.1630056E-03 2.2955894E-02 at 170iterations 6.6041778E-04 1.4648438E-02 at 180iterations finished qdiffx linear iterations at : 15:11:54 total time elapsed so far: 17.89000 # loops : 180 mean,max change (kT/e) : 6.6041778E-04 1.4648438E-02 energy calculations done at 17.89000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.12000 DelPhi exited at 15:11:55 18.122u 0.459s 0:18.87 98.4% 0+0k 0+0io 0pf+0w