Tue Oct 11 06:36:43 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 06:36:43 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: 261 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2056 !!! WARNING: SEP 190 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7077253 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): -20.18400 24.61000 ymin,ymax (A): -28.62100 12.09900 zmin,zma (A): -13.50500 36.79700 x,y,z range (A): 44.79400 40.72000 50.30200 scale (grids/A): 0.7077253 object centre (A): 2.213000 -8.261000 11.64600 number of atom coordinates read : 2056 total number of charged atoms : 1926 net assigned charge : 7.025010 assigned positive charge : 312.4891 centred at (gu) : 89.84563 90.23244 89.36921 assigned negative charge : -305.4641 centred at (gu) : 89.66326 90.21011 89.34154 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 6933 nv = 96 ne = 84 npr = 41388 no. pairs analyzed = 41388 no. exposed pairs = 2490 no. arc points = 16864 no. surface atoms = 842 nbur = 1214 mkacc time = 7.0000008E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 449 mr = 3995 m= 2 mr = 74 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1600000 number of dielectric boundary points 3315 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1590 ## 152 charges are in solution ## iepsmp to db, and charging done at 0.2300000 number of grid points assigned charge 7721 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.2212691E-08 6.5157906E-08 midg,1,midg; midg,igrid,midg 4.7005290E-08 7.4035810E-08 1,midg,midg; igrid,midg,midg -3.1582196E-08 1.4287249E-07 gauss-seidel spectral radius is 0.9895894 estimated iterations to convergence 80 setup time was (sec) 0.3500000 now iterating at: 06:36:44 rms-change max change #iterations 0.1973801 32.41066 at 10iterations 2.4883311E-02 3.453000 at 20iterations 3.2879231E-03 0.4864836 at 30iterations 5.1438605E-04 6.8637848E-02 at 40iterations 1.1899928E-04 1.6107559E-02 at 50iterations finished qdiffx linear iterations at : 06:36:47 total time elapsed so far: 3.210000 # loops : 50 mean,max change (kT/e) : 1.1899928E-04 1.6107559E-02 energy calculations done at 3.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.340000 DelPhi exited at 06:36:47 3.344u 0.167s 0:03.98 87.9% 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 06:36:47 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: 261 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2056 !!! WARNING: SEP 190 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.123176 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): -20.18400 24.61000 ymin,ymax (A): -28.62100 12.09900 zmin,zma (A): -13.50500 36.79700 x,y,z range (A): 44.79400 40.72000 50.30200 scale (grids/A): 2.123176 object centre (A): 2.213000 -8.261000 11.64600 number of atom coordinates read : 2056 total number of charged atoms : 1926 net assigned charge : 7.025010 assigned positive charge : 312.4891 centred at (gu) : 89.53687 90.69745 88.10778 assigned negative charge : -305.4641 centred at (gu) : 88.98990 90.63037 88.02469 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 73979 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16864 grid for indexing accessible points = 1.400000 m= 29402 mr = 52708 m= 5647 mr = 22223 m= 483 mr = 3735 m= 18 mr = 251 m= 0 mr = 3 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 30609 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 78 iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 15308 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) : 0.7077253 object centre at (A) : 2.213000 -8.261000 11.64600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.6923924E-02 4.1736398E-02 midg,1,midg; midg,igrid,midg 4.4908249E-03 3.0216254E-02 1,midg,midg; igrid,midg,midg 1.2808529E-02 3.9783020E-02 gauss-seidel spectral radius is 0.9988287 estimated iterations to convergence 231 setup time was (sec) 0.5800000 now iterating at: 06:36:48 rms-change max change #iterations 4.574402 193.2044 at 10iterations 2.259772 77.60918 at 20iterations 1.120420 34.60817 at 30iterations 0.5552763 16.98651 at 40iterations 0.2767851 8.343102 at 50iterations 0.1373473 4.219936 at 60iterations 6.8196334E-02 2.135486 at 70iterations 3.3799451E-02 1.010017 at 80iterations 1.6863354E-02 0.4759140 at 90iterations 8.4564267E-03 0.2632942 at 100iterations 4.2369822E-03 0.1340027 at 110iterations 2.1550073E-03 6.8511963E-02 at 120iterations finished qdiffx linear iterations at : 06:36:55 total time elapsed so far: 7.620000 # loops : 120 mean,max change (kT/e) : 2.1550073E-03 6.8511963E-02 energy calculations done at 7.620000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.750000 DelPhi exited at 06:36:56 7.749u 0.208s 0:08.42 94.2% 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 06:36:56 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: 261 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2056 !!! WARNING: SEP 190 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.184764 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): -20.18400 24.61000 ymin,ymax (A): -28.62100 12.09900 zmin,zma (A): -13.50500 36.79700 x,y,z range (A): 44.79400 40.72000 50.30200 scale (grids/A): 3.184764 object centre (A): 2.213000 -8.261000 11.64600 number of atom coordinates read : 2056 total number of charged atoms : 1926 net assigned charge : 7.025010 assigned positive charge : 312.4891 centred at (gu) : 89.30529 91.04606 87.16171 assigned negative charge : -305.4641 centred at (gu) : 88.48478 90.94563 87.03704 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 170811 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16864 grid for indexing accessible points = 1.400000 m= 91875 mr = 127033 m= 37112 mr = 76396 m= 10624 mr = 30472 m= 2068 mr = 8241 m= 240 mr = 1465 m= 4 mr = 155 m= 0 mr = 0 time to grow re-entrant surface = 0.5800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.140000 number of dielectric boundary points 68972 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.220000 number of grid points assigned charge 15408 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) : 2.123176 object centre at (A) : 2.213000 -8.261000 11.64600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.7084324 0.3347524 midg,1,midg; midg,igrid,midg 2.0946722E-02 0.2280112 1,midg,midg; igrid,midg,midg 0.2367967 0.2948329 gauss-seidel spectral radius is 0.9992921 estimated iterations to convergence 297 setup time was (sec) 1.370000 now iterating at: 06:36:57 rms-change max change #iterations 10.17221 311.5135 at 10iterations 5.997962 191.6194 at 20iterations 3.541662 77.54240 at 30iterations 2.084688 37.51706 at 40iterations 1.224437 24.64757 at 50iterations 0.7188903 13.33832 at 60iterations 0.4211607 8.175930 at 70iterations 0.2465480 4.015528 at 80iterations 0.1444756 2.891735 at 90iterations 8.4680609E-02 1.771528 at 100iterations 4.9555443E-02 0.8986778 at 110iterations 2.9257502E-02 0.5033798 at 120iterations 1.7323824E-02 0.3028488 at 130iterations 1.0401134E-02 0.1830616 at 140iterations 6.3881045E-03 0.1192932 at 150iterations 4.0428708E-03 8.7142944E-02 at 160iterations 2.6937071E-03 5.3234100E-02 at 170iterations 1.8923526E-03 3.6720276E-02 at 180iterations finished qdiffx linear iterations at : 06:37:09 total time elapsed so far: 12.54000 # loops : 180 mean,max change (kT/e) : 1.8923526E-03 3.6720276E-02 energy calculations done at 12.54000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.67000 DelPhi exited at 06:37:09 12.668u 0.215s 0:13.18 97.6% 0+0k 0+0io 0pf+0w