Thu Jan 19 13:33:28 PST 2012 #!/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 Thu Jan 19 2012 at 13:33:28 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: 329 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 6895 !!! WARNING: HIZ 357 has a net charge of 0.2000 !!! WARNING: HEM 1105 has a net charge of -4.0000 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: 0.4369438 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): -2.108000 79.36700 ymin,ymax (A): -11.90100 65.41200 zmin,zma (A): -23.57400 43.11500 x,y,z range (A): 81.47501 77.31300 66.68900 scale (grids/A): 0.4369438 object centre (A): 38.62950 26.75550 9.770499 number of atom coordinates read : 6895 total number of charged atoms : 6723 net assigned charge : 0.2000419 assigned positive charge : 1052.385 centred at (gu) : 87.60811 90.27843 89.55397 assigned negative charge : -1052.193 centred at (gu) : 87.53116 90.34252 89.45717 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7658 nv = 96 ne = 84 npr = 141419 no. pairs analyzed = 141419 no. exposed pairs = 8725 no. arc points = 59460 no. surface atoms = 2907 nbur = 3988 mkacc time = 0.2400000 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 = 1.904000 m= 187 mr = 3673 m= 0 mr = 2 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 3 time to turn everything in is 0.4500000 number of dielectric boundary points 4170 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4992 ## 1038 charges are in solution ## iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 10611 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.0403282E-11 8.2367117E-12 midg,1,midg; midg,igrid,midg 5.8721908E-12 -6.3816057E-12 1,midg,midg; igrid,midg,midg -1.5056243E-11 3.6716710E-12 gauss-seidel spectral radius is 0.9734156 estimated iterations to convergence 51 setup time was (sec) 0.6600000 now iterating at: 13:33:32 rms-change max change #iterations 3.4204289E-02 6.188007 at 10iterations 1.8183530E-03 0.2753639 at 20iterations 5.5385125E-04 9.5756531E-02 at 30iterations 2.3071768E-04 4.0467262E-02 at 40iterations 9.8145531E-05 1.7213821E-02 at 50iterations finished qdiffx linear iterations at : 13:33:42 total time elapsed so far: 3.850000 # loops : 50 mean,max change (kT/e) : 9.8145531E-05 1.7213821E-02 energy calculations done at 3.850000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.970000 DelPhi exited at 13:33:44 3.978u 0.215s 0:15.26 27.3% 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 Thu Jan 19 2012 at 13:33:45 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: 329 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 6895 !!! WARNING: HIZ 357 has a net charge of 0.2000 !!! WARNING: HEM 1105 has a net charge of -4.0000 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: 1.310831 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): -2.108000 79.36700 ymin,ymax (A): -11.90100 65.41200 zmin,zma (A): -23.57400 43.11500 x,y,z range (A): 81.47501 77.31300 66.68900 scale (grids/A): 1.310831 object centre (A): 38.62950 26.75550 9.770499 number of atom coordinates read : 6895 total number of charged atoms : 6723 net assigned charge : 0.2000419 assigned positive charge : 1052.385 centred at (gu) : 82.82224 90.83356 88.65981 assigned negative charge : -1052.193 centred at (gu) : 82.59290 91.02735 88.37115 start vw surface at 0.1700000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 89056 reading accessible surface arcs data from file ARCDAT no. of arc points read = 59460 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.792000 m= 19978 mr = 58776 m= 898 mr = 11749 m= 10 mr = 213 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 1063 time to turn everything in is 0.4700000 number of dielectric boundary points 39204 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1037 ## 29 charges are in solution ## iepsmp to db, and charging done at 0.5600000 number of grid points assigned charge 46972 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) : 0.4369438 object centre at (A) : 38.62950 26.75550 9.770499 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.3671997E-03 2.6320932E-03 midg,1,midg; midg,igrid,midg 6.3506989E-03 1.2491060E-03 1,midg,midg; igrid,midg,midg -1.8267332E-02 1.1401362E-03 gauss-seidel spectral radius is 0.9974992 estimated iterations to convergence 159 setup time was (sec) 0.7000000 now iterating at: 13:33:48 rms-change max change #iterations 3.216378 148.4879 at 10iterations 1.148165 42.84949 at 20iterations 0.4130178 15.41265 at 30iterations 0.1490263 5.345368 at 40iterations 5.3414322E-02 1.944858 at 50iterations 1.9295840E-02 0.7228355 at 60iterations 6.9439267E-03 0.2289848 at 70iterations 2.5644880E-03 8.3537102E-02 at 80iterations 9.8948926E-04 3.5175800E-02 at 90iterations 4.3891143E-04 1.6633034E-02 at 100iterations 2.4238776E-04 8.1939697E-03 at 110iterations 1.5891615E-04 5.1755905E-03 at 120iterations finished qdiffx linear iterations at : 13:34:06 total time elapsed so far: 8.470000 # loops : 120 mean,max change (kT/e) : 1.5891615E-04 5.1755905E-03 energy calculations done at 8.470000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.610000 DelPhi exited at 13:34:08 8.612u 0.235s 0:23.07 38.3% 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 Thu Jan 19 2012 at 13:34:09 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: 329 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 6895 !!! WARNING: HIZ 357 has a net charge of 0.2000 !!! WARNING: HEM 1105 has a net charge of -4.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 1.966247 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): -2.108000 79.36700 ymin,ymax (A): -11.90100 65.41200 zmin,zma (A): -23.57400 43.11500 x,y,z range (A): 81.47501 77.31300 66.68900 scale (grids/A): 1.966247 object centre (A): 38.62950 26.75550 9.770499 number of atom coordinates read : 6895 total number of charged atoms : 6723 net assigned charge : 0.2000419 assigned positive charge : 1052.385 centred at (gu) : 79.23304 91.24982 87.98929 assigned negative charge : -1052.193 centred at (gu) : 78.88927 91.54085 87.55665 start vw surface at 0.1700000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 209160 reading accessible surface arcs data from file ARCDAT no. of arc points read = 59460 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.764000 m= 78474 mr = 146739 m= 13429 mr = 57780 m= 907 mr = 8509 m= 9 mr = 360 m= 0 mr = 0 time to grow re-entrant surface = 0.5799999 no. cavity mid-points inaccessible to solvent = 3588 time to turn everything in is 1.100000 number of dielectric boundary points 88591 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 296 iepsmp to db, and charging done at 1.220000 number of grid points assigned charge 53114 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) : 1.310831 object centre at (A) : 38.62950 26.75550 9.770499 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1044378 6.2674068E-02 midg,1,midg; midg,igrid,midg 0.2367759 8.8259205E-02 1,midg,midg; igrid,midg,midg -0.5333169 6.1161429E-02 gauss-seidel spectral radius is 0.9990118 estimated iterations to convergence 252 setup time was (sec) 1.410000 now iterating at: 13:34:12 rms-change max change #iterations 9.764915 312.5296 at 10iterations 5.324195 149.3268 at 20iterations 2.882900 69.66182 at 30iterations 1.555264 34.22277 at 40iterations 0.8331806 18.49859 at 50iterations 0.4453709 9.341217 at 60iterations 0.2376211 5.803680 at 70iterations 0.1264599 2.682585 at 80iterations 6.7119375E-02 1.587764 at 90iterations 3.5572421E-02 0.7016592 at 100iterations 1.8889671E-02 0.3827820 at 110iterations 9.9999253E-03 0.2033014 at 120iterations 5.3124665E-03 0.1146383 at 130iterations 2.8270769E-03 6.4369202E-02 at 140iterations 1.5072193E-03 3.2072067E-02 at 150iterations 8.1539678E-04 1.6962528E-02 at 160iterations 4.5106694E-04 9.8791122E-03 at 170iterations 2.6183389E-04 5.5809021E-03 at 180iterations finished qdiffx linear iterations at : 13:34:54 total time elapsed so far: 15.01000 # loops : 180 mean,max change (kT/e) : 2.6183389E-04 5.5809021E-03 energy calculations done at 15.01000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.14000 DelPhi exited at 13:34:54 15.145u 0.291s 0:45.25 34.0% 0+0k 0+0io 0pf+0w