Sun Oct 9 06:07:03 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 Sun Oct 9 2011 at 06:07:03 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: 234 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2420 !!! WARNING: HIZ 132 has a net charge of 0.2000 !!! WARNING: HIZ 136 has a net charge of 0.2000 !!! WARNING: HIZ 296 has a net charge of 0.2000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5917947 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): -36.90100 23.25500 ymin,ymax (A): -20.58300 34.58100 zmin,zma (A): -38.60800 5.330000 x,y,z range (A): 60.15600 55.16400 43.93800 scale (grids/A): 0.5917947 object centre (A): -6.823001 6.998999 -16.63900 number of atom coordinates read : 2420 total number of charged atoms : 2274 net assigned charge : 0.1000160 assigned positive charge : 379.9173 centred at (gu) : 89.56729 91.27045 90.70245 assigned negative charge : -379.8178 centred at (gu) : 89.94094 91.60385 90.68723 start vw surface at 0.1700000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 5831 nv = 96 ne = 84 npr = 45290 no. pairs analyzed = 45290 no. exposed pairs = 3462 no. arc points = 25521 no. surface atoms = 1138 nbur = 1282 mkacc time = 0.1200000 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= 281 mr = 2754 m= 2 mr = 10 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 3350 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2536 ## 287 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 7140 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.2926909E-10 6.6825123E-10 midg,1,midg; midg,igrid,midg 6.6836594E-09 -1.2684661E-08 1,midg,midg; igrid,midg,midg 1.1058321E-08 -9.5739399E-09 gauss-seidel spectral radius is 0.9852260 estimated iterations to convergence 67 setup time was (sec) 0.5900000 now iterating at: 06:07:04 rms-change max change #iterations 9.7247444E-02 20.98138 at 10iterations 7.7580214E-03 1.278910 at 20iterations 6.2457722E-04 9.7564697E-02 at 30iterations 5.1980292E-05 7.1449280E-03 at 40iterations 4.4927842E-06 7.5149536E-04 at 50iterations finished qdiffx linear iterations at : 06:07:07 total time elapsed so far: 3.960000 # loops : 50 mean,max change (kT/e) : 4.4927842E-06 7.5149536E-04 energy calculations done at 3.960000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.140000 DelPhi exited at 06:07:08 4.146u 0.274s 0:04.69 94.0% 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 Sun Oct 9 2011 at 06:07:08 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: 234 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2420 !!! WARNING: HIZ 132 has a net charge of 0.2000 !!! WARNING: HIZ 136 has a net charge of 0.2000 !!! WARNING: HIZ 296 has a net charge of 0.2000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.775384 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): -36.90100 23.25500 ymin,ymax (A): -20.58300 34.58100 zmin,zma (A): -38.60800 5.330000 x,y,z range (A): 60.15600 55.16400 43.93800 scale (grids/A): 1.775384 object centre (A): -6.823001 6.998999 -16.63900 number of atom coordinates read : 2420 total number of charged atoms : 2274 net assigned charge : 0.1000160 assigned positive charge : 379.9173 centred at (gu) : 88.70135 93.81115 92.10708 assigned negative charge : -379.8178 centred at (gu) : 89.82269 94.81142 92.06184 start vw surface at 0.1500000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 62872 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25521 grid for indexing accessible points = 1.400000 m= 19920 mr = 39851 m= 2448 mr = 13344 m= 94 mr = 1182 m= 0 mr = 19 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 479 time to turn everything in is 0.5700000 number of dielectric boundary points 30938 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 272 iepsmp to db, and charging done at 0.6900000 number of grid points assigned charge 17704 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) : 0.5917947 object centre at (A) : -6.823001 6.998999 -16.63900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.1348074E-04 4.0041353E-03 midg,1,midg; midg,igrid,midg 3.4307774E-02 -3.3624519E-02 1,midg,midg; igrid,midg,midg 3.3459812E-02 -3.3852592E-02 gauss-seidel spectral radius is 0.9984325 estimated iterations to convergence 200 setup time was (sec) 0.8500000 now iterating at: 06:07:09 rms-change max change #iterations 3.670411 171.8912 at 10iterations 1.618097 66.62193 at 20iterations 0.7163799 25.76335 at 30iterations 0.3148034 12.03643 at 40iterations 0.1393741 5.310388 at 50iterations 6.1531022E-02 2.120735 at 60iterations 2.7227815E-02 1.013674 at 70iterations 1.2028656E-02 0.4730821 at 80iterations 5.3158016E-03 0.1905632 at 90iterations 2.3550382E-03 8.1054688E-02 at 100iterations 1.0400960E-03 3.7325859E-02 at 110iterations 4.6105630E-04 1.8196106E-02 at 120iterations finished qdiffx linear iterations at : 06:07:18 total time elapsed so far: 9.390000 # loops : 120 mean,max change (kT/e) : 4.6105630E-04 1.8196106E-02 energy calculations done at 9.390000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.570000 DelPhi exited at 06:07:18 9.569u 0.338s 0:10.18 97.1% 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 Sun Oct 9 2011 at 06:07:18 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: 234 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2420 !!! WARNING: HIZ 132 has a net charge of 0.2000 !!! WARNING: HIZ 136 has a net charge of 0.2000 !!! WARNING: HIZ 296 has a net charge of 0.2000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.663076 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): -36.90100 23.25500 ymin,ymax (A): -20.58300 34.58100 zmin,zma (A): -38.60800 5.330000 x,y,z range (A): 60.15600 55.16400 43.93800 scale (grids/A): 2.663076 object centre (A): -6.823001 6.998999 -16.63900 number of atom coordinates read : 2420 total number of charged atoms : 2274 net assigned charge : 0.1000160 assigned positive charge : 379.9173 centred at (gu) : 88.05183 95.71650 93.16058 assigned negative charge : -379.8178 centred at (gu) : 89.73416 97.21712 93.09266 start vw surface at 0.1600000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 145428 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25521 grid for indexing accessible points = 1.400000 m= 66843 mr = 97950 m= 20664 mr = 51535 m= 3944 mr = 15156 m= 368 mr = 2500 m= 10 mr = 179 m= 0 mr = 0 time to grow re-entrant surface = 0.8300000 no. cavity mid-points inaccessible to solvent = 1604 time to turn everything in is 1.410000 number of dielectric boundary points 69937 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 7 iepsmp to db, and charging done at 1.550000 number of grid points assigned charge 18190 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) : 1.775384 object centre at (A) : -6.823001 6.998999 -16.63900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.7098163E-03 4.7512859E-02 midg,1,midg; midg,igrid,midg 0.4542980 -0.5156668 1,midg,midg; igrid,midg,midg 0.3831226 -0.5493665 gauss-seidel spectral radius is 0.9992163 estimated iterations to convergence 282 setup time was (sec) 1.720000 now iterating at: 06:07:20 rms-change max change #iterations 9.188128 264.1989 at 10iterations 5.333447 133.2653 at 20iterations 3.058218 87.17357 at 30iterations 1.746064 40.24173 at 40iterations 0.9958142 20.37701 at 50iterations 0.5661736 14.13339 at 60iterations 0.3216661 7.534721 at 70iterations 0.1816560 4.046177 at 80iterations 0.1032011 2.282762 at 90iterations 5.8144011E-02 1.147072 at 100iterations 3.2905970E-02 0.6828308 at 110iterations 1.8606963E-02 0.3826342 at 120iterations 1.0490125E-02 0.2094498 at 130iterations 5.9326929E-03 0.1301689 at 140iterations 3.3443705E-03 7.0457458E-02 at 150iterations 1.8852402E-03 3.8898468E-02 at 160iterations 1.0659039E-03 2.2157669E-02 at 170iterations 6.0058699E-04 1.2730598E-02 at 180iterations finished qdiffx linear iterations at : 06:07:34 total time elapsed so far: 15.68000 # loops : 180 mean,max change (kT/e) : 6.0058699E-04 1.2730598E-02 energy calculations done at 15.68000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.86000 DelPhi exited at 06:07:35 15.861u 0.336s 0:16.47 98.2% 0+0k 0+0io 0pf+0w