Mon Oct 10 17:03:38 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 Mon Oct 10 2011 at 17:03:38 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2988 !!! WARNING: HIZ 83 has a net charge of 0.2000 !!! WARNING: HIZ 119 has a net charge of 0.2000 !!! WARNING: MG9 961 has a net charge of 1.4000 !!! WARNING: ZN9 964 has a net charge of 1.4000 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: 0.5973154 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): -1.266000 55.04200 ymin,ymax (A): 96.97900 153.6320 zmin,zma (A): -15.74400 43.85600 x,y,z range (A): 56.30800 56.65299 59.60000 scale (grids/A): 0.5973154 object centre (A): 26.88800 125.3055 14.05600 number of atom coordinates read : 2988 total number of charged atoms : 2843 net assigned charge : 3.700027 assigned positive charge : 454.1440 centred at (gu) : 88.96360 89.66347 91.01176 assigned negative charge : -450.4454 centred at (gu) : 89.09952 89.68008 91.07159 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6935 nv = 96 ne = 84 npr = 60837 no. pairs analyzed = 60837 no. exposed pairs = 3854 no. arc points = 27554 no. surface atoms = 1284 nbur = 1704 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 313 mr = 3545 m= 1 mr = 24 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2200000 number of dielectric boundary points 3680 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2838 ## 339 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 8890 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.9639511E-09 -1.1969775E-09 midg,1,midg; midg,igrid,midg 2.2221478E-09 7.1585798E-10 1,midg,midg; igrid,midg,midg 8.4087439E-09 -3.0983580E-09 gauss-seidel spectral radius is 0.9855320 estimated iterations to convergence 68 setup time was (sec) 0.4100000 now iterating at: 17:03:39 rms-change max change #iterations 0.1141004 19.76171 at 10iterations 9.7262654E-03 1.728569 at 20iterations 8.2330522E-04 0.1240988 at 30iterations 8.7015185E-05 1.5186310E-02 at 40iterations 1.5146388E-05 2.2974014E-03 at 50iterations finished qdiffx linear iterations at : 17:03:42 total time elapsed so far: 3.270000 # loops : 50 mean,max change (kT/e) : 1.5146388E-05 2.2974014E-03 energy calculations done at 3.270000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.390000 DelPhi exited at 17:03:42 3.397u 0.179s 0:03.91 91.0% 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 Mon Oct 10 2011 at 17:03:43 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2988 !!! WARNING: HIZ 83 has a net charge of 0.2000 !!! WARNING: HIZ 119 has a net charge of 0.2000 !!! WARNING: MG9 961 has a net charge of 1.4000 !!! WARNING: ZN9 964 has a net charge of 1.4000 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: 1.791946 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): -1.266000 55.04200 ymin,ymax (A): 96.97900 153.6320 zmin,zma (A): -15.74400 43.85600 x,y,z range (A): 56.30800 56.65299 59.60000 scale (grids/A): 1.791946 object centre (A): 26.88800 125.3055 14.05600 number of atom coordinates read : 2988 total number of charged atoms : 2843 net assigned charge : 3.700027 assigned positive charge : 454.1440 centred at (gu) : 86.88975 88.98940 93.03443 assigned negative charge : -450.4454 centred at (gu) : 87.29842 89.04002 93.21446 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 76252 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27554 grid for indexing accessible points = 1.400000 m= 24534 mr = 51113 m= 3516 mr = 17043 m= 158 mr = 2018 m= 3 mr = 30 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 266 time to turn everything in is 0.3700000 number of dielectric boundary points 34259 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 257 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 22173 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) : 0.5973154 object centre at (A) : 26.88800 125.3055 14.05600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.5593517E-02 -9.9088596E-03 midg,1,midg; midg,igrid,midg 1.6771380E-02 -1.9535059E-03 1,midg,midg; igrid,midg,midg 2.1927884E-02 -2.4063712E-02 gauss-seidel spectral radius is 0.9985112 estimated iterations to convergence 206 setup time was (sec) 0.5800000 now iterating at: 17:03:43 rms-change max change #iterations 4.103024 171.9767 at 10iterations 1.858618 64.08880 at 20iterations 0.8374901 27.62247 at 30iterations 0.3801428 11.69257 at 40iterations 0.1711899 5.244213 at 50iterations 7.7715360E-02 2.584576 at 60iterations 3.5244092E-02 1.159714 at 70iterations 1.5906947E-02 0.4967551 at 80iterations 7.2000483E-03 0.2633395 at 90iterations 3.2749374E-03 0.1032257 at 100iterations 1.4811652E-03 4.8484802E-02 at 110iterations 6.7227642E-04 2.2186279E-02 at 120iterations finished qdiffx linear iterations at : 17:03:50 total time elapsed so far: 7.660000 # loops : 120 mean,max change (kT/e) : 6.7227642E-04 2.2186279E-02 energy calculations done at 7.660000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.790000 DelPhi exited at 17:03:52 7.794u 0.207s 0:09.14 87.4% 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 Mon Oct 10 2011 at 17:03:52 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2988 !!! WARNING: HIZ 83 has a net charge of 0.2000 !!! WARNING: HIZ 119 has a net charge of 0.2000 !!! WARNING: MG9 961 has a net charge of 1.4000 !!! WARNING: ZN9 964 has a net charge of 1.4000 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: 2.687920 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): -1.266000 55.04200 ymin,ymax (A): 96.97900 153.6320 zmin,zma (A): -15.74400 43.85600 x,y,z range (A): 56.30800 56.65299 59.60000 scale (grids/A): 2.687920 object centre (A): 26.88800 125.3055 14.05600 number of atom coordinates read : 2988 total number of charged atoms : 2843 net assigned charge : 3.700027 assigned positive charge : 454.1440 centred at (gu) : 85.33449 88.48395 94.55154 assigned negative charge : -450.4454 centred at (gu) : 85.94749 88.55988 94.82177 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 176720 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27554 grid for indexing accessible points = 1.400000 m= 81777 mr = 124902 m= 26903 mr = 64721 m= 5955 mr = 20477 m= 691 mr = 4280 m= 23 mr = 407 m= 1 mr = 4 m= 0 mr = 0 time to grow re-entrant surface = 0.5200000 no. cavity mid-points inaccessible to solvent = 834 time to turn everything in is 0.9300000 number of dielectric boundary points 77279 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.020000 number of grid points assigned charge 22739 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) : 1.791946 object centre at (A) : 26.88800 125.3055 14.05600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3194509 -0.1135951 midg,1,midg; midg,igrid,midg 0.2122135 -2.9655149E-02 1,midg,midg; igrid,midg,midg 0.1519557 -0.3672456 gauss-seidel spectral radius is 0.9992383 estimated iterations to convergence 286 setup time was (sec) 1.170000 now iterating at: 17:03:53 rms-change max change #iterations 9.976590 285.0009 at 10iterations 5.786190 123.4186 at 20iterations 3.326232 67.88287 at 30iterations 1.910957 40.09749 at 40iterations 1.094158 25.43997 at 50iterations 0.6250187 13.03992 at 60iterations 0.3583180 6.912178 at 70iterations 0.2040733 3.963055 at 80iterations 0.1165945 2.332924 at 90iterations 6.6575475E-02 1.506421 at 100iterations 3.7890404E-02 0.6973333 at 110iterations 2.1642528E-02 0.3962517 at 120iterations 1.2308286E-02 0.2205696 at 130iterations 7.0088813E-03 0.1319885 at 140iterations 3.9992495E-03 7.2559357E-02 at 150iterations 2.2870437E-03 4.1195869E-02 at 160iterations 1.3012534E-03 2.5455475E-02 at 170iterations 7.4504828E-04 1.3741493E-02 at 180iterations finished qdiffx linear iterations at : 17:04:04 total time elapsed so far: 12.51000 # loops : 180 mean,max change (kT/e) : 7.4504828E-04 1.3741493E-02 energy calculations done at 12.51000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.64000 DelPhi exited at 17:04:05 12.646u 0.225s 0:13.35 96.3% 0+0k 0+0io 0pf+0w