Tue Oct 11 06:11:45 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 Tue Oct 11 2011 at 06:11:45 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: 274 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2051 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 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: 0.7612856 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): -18.03600 28.26700 ymin,ymax (A): -11.63600 31.03000 zmin,zma (A): -9.033999 37.72900 x,y,z range (A): 46.30300 42.66600 46.76300 scale (grids/A): 0.7612856 object centre (A): 5.115500 9.697001 14.34750 number of atom coordinates read : 2051 total number of charged atoms : 1919 net assigned charge : 7.931008 assigned positive charge : 311.9721 centred at (gu) : 90.55411 90.01208 91.31905 assigned negative charge : -304.0411 centred at (gu) : 90.44295 89.94823 91.14983 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 8147 nv = 96 ne = 84 npr = 41181 no. pairs analyzed = 41181 no. exposed pairs = 2525 no. arc points = 17005 no. surface atoms = 859 nbur = 1192 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 678 mr = 4776 m= 4 mr = 145 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 11 time to turn everything in is 0.3100000 number of dielectric boundary points 3908 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1376 ## 121 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 8466 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.7440867E-08 5.8451531E-07 midg,1,midg; midg,igrid,midg 1.1953738E-07 3.0822784E-07 1,midg,midg; igrid,midg,midg 4.5571053E-08 4.1563442E-07 gauss-seidel spectral radius is 0.9909925 estimated iterations to convergence 86 setup time was (sec) 0.5800000 now iterating at: 06:11:46 rms-change max change #iterations 0.2690873 33.76914 at 10iterations 3.9211363E-02 4.483220 at 20iterations 5.7509504E-03 0.6519685 at 30iterations 9.7539701E-04 0.1180248 at 40iterations 2.2709138E-04 2.7303696E-02 at 50iterations finished qdiffx linear iterations at : 06:11:49 total time elapsed so far: 3.870000 # loops : 50 mean,max change (kT/e) : 2.2709138E-04 2.7303696E-02 energy calculations done at 3.870000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.040000 DelPhi exited at 06:11:50 4.048u 0.256s 0:04.65 92.2% 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 Tue Oct 11 2011 at 06:11:50 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: 274 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2051 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 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: 2.283857 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): -18.03600 28.26700 ymin,ymax (A): -11.63600 31.03000 zmin,zma (A): -9.033999 37.72900 x,y,z range (A): 46.30300 42.66600 46.76300 scale (grids/A): 2.283857 object centre (A): 5.115500 9.697001 14.34750 number of atom coordinates read : 2051 total number of charged atoms : 1919 net assigned charge : 7.931008 assigned positive charge : 311.9721 centred at (gu) : 91.66221 90.03637 93.95726 assigned negative charge : -304.0411 centred at (gu) : 91.32897 89.84465 93.44967 start vw surface at 0.1600000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 85132 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17005 grid for indexing accessible points = 1.400000 m= 37636 mr = 60853 m= 8948 mr = 29138 m= 1199 mr = 6305 m= 56 mr = 710 m= 1 mr = 7 m= 0 mr = 0 time to grow re-entrant surface = 0.4400000 no. cavity mid-points inaccessible to solvent = 304 time to turn everything in is 0.8200000 number of dielectric boundary points 35959 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 35 iepsmp to db, and charging done at 0.9700000 number of grid points assigned charge 15303 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) : 0.7612856 object centre at (A) : 5.115500 9.697001 14.34750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.4451115E-02 7.6091066E-02 midg,1,midg; midg,igrid,midg 3.8086072E-02 3.2658476E-02 1,midg,midg; igrid,midg,midg 5.0444305E-02 0.1192290 gauss-seidel spectral radius is 0.9989623 estimated iterations to convergence 246 setup time was (sec) 1.120000 now iterating at: 06:11:51 rms-change max change #iterations 5.152294 215.7203 at 10iterations 2.674910 94.74292 at 20iterations 1.382218 36.11832 at 30iterations 0.7154920 19.95202 at 40iterations 0.3705335 9.685787 at 50iterations 0.1915912 5.888990 at 60iterations 9.9118359E-02 2.855518 at 70iterations 5.1369868E-02 1.348020 at 80iterations 2.6673565E-02 0.7957802 at 90iterations 1.3872836E-02 0.4299479 at 100iterations 7.3043834E-03 0.2022591 at 110iterations 3.8847984E-03 0.1160355 at 120iterations finished qdiffx linear iterations at : 06:11:59 total time elapsed so far: 9.490000 # loops : 120 mean,max change (kT/e) : 3.8847984E-03 0.1160355 energy calculations done at 9.490000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.660000 DelPhi exited at 06:12:00 9.662u 0.290s 0:10.26 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 Tue Oct 11 2011 at 06:12:00 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: 274 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2051 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 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: 3.425785 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): -18.03600 28.26700 ymin,ymax (A): -11.63600 31.03000 zmin,zma (A): -9.033999 37.72900 x,y,z range (A): 46.30300 42.66600 46.76300 scale (grids/A): 3.425785 object centre (A): 5.115500 9.697001 14.34750 number of atom coordinates read : 2051 total number of charged atoms : 1919 net assigned charge : 7.931008 assigned positive charge : 311.9721 centred at (gu) : 92.49323 90.05442 95.93597 assigned negative charge : -304.0411 centred at (gu) : 91.99357 89.76701 95.17449 start vw surface at 0.1400000 fill in re-entrant regions at 1.130000 boundary points on vw surface= 195811 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17005 grid for indexing accessible points = 1.400000 m= 112117 mr = 145933 m= 51585 mr = 94136 m= 17512 mr = 43189 m= 4511 mr = 13898 m= 853 mr = 3465 m= 64 mr = 614 m= 0 mr = 22 time to grow re-entrant surface = 1.390000 no. cavity mid-points inaccessible to solvent = 984 time to turn everything in is 2.660000 number of dielectric boundary points 81196 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.820000 number of grid points assigned charge 15352 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) : 2.283857 object centre at (A) : 5.115500 9.697001 14.34750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.5852096 0.6154521 midg,1,midg; midg,igrid,midg 0.2603832 0.1137050 1,midg,midg; igrid,midg,midg 0.3404877 0.8067564 gauss-seidel spectral radius is 0.9993319 estimated iterations to convergence 305 setup time was (sec) 2.990000 now iterating at: 06:12:03 rms-change max change #iterations 11.07422 386.4537 at 10iterations 6.701747 129.0607 at 20iterations 4.026569 71.53526 at 30iterations 2.409106 44.79751 at 40iterations 1.438619 24.27976 at 50iterations 0.8599080 14.03196 at 60iterations 0.5118756 8.391384 at 70iterations 0.3049195 5.067474 at 80iterations 0.1814007 2.894485 at 90iterations 0.1080862 1.797855 at 100iterations 6.4442031E-02 0.9925957 at 110iterations 3.8549900E-02 0.6996307 at 120iterations 2.3251129E-02 0.4095840 at 130iterations 1.4263706E-02 0.2403755 at 140iterations 9.0203425E-03 0.1634083 at 150iterations 5.9481496E-03 0.1024132 at 160iterations 4.1633993E-03 7.2006226E-02 at 170iterations 3.1098058E-03 5.3142548E-02 at 180iterations finished qdiffx linear iterations at : 06:12:17 total time elapsed so far: 17.19000 # loops : 180 mean,max change (kT/e) : 3.1098058E-03 5.3142548E-02 energy calculations done at 17.19000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.37000 DelPhi exited at 06:12:18 17.373u 0.322s 0:18.26 96.8% 0+0k 0+0io 0pf+0w