Sat Oct 15 15:12:06 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 Sat Oct 15 2011 at 15:12:06 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2734 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6678172 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): -12.06500 37.46200 ymin,ymax (A): -26.57300 21.47200 zmin,zma (A): -7.925000 45.38300 x,y,z range (A): 49.52700 48.04500 53.30800 scale (grids/A): 0.6678172 object centre (A): 12.69850 -2.550500 18.72900 number of atom coordinates read : 2734 total number of charged atoms : 2587 net assigned charge : 7.500018 assigned positive charge : 412.1918 centred at (gu) : 90.36906 90.41718 91.19647 assigned negative charge : -404.6924 centred at (gu) : 90.12806 90.25165 91.30429 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 8034 nv = 96 ne = 84 npr = 56592 no. pairs analyzed = 56592 no. exposed pairs = 3219 no. arc points = 22220 no. surface atoms = 1092 nbur = 1642 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 445 mr = 4599 m= 3 mr = 67 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 60 time to turn everything in is 0.2000000 number of dielectric boundary points 3816 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2265 ## 207 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 9598 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.9439364E-08 -5.4203579E-09 midg,1,midg; midg,igrid,midg -1.7101197E-08 7.0158407E-08 1,midg,midg; igrid,midg,midg -3.5590389E-08 8.9089205E-08 gauss-seidel spectral radius is 0.9883823 estimated iterations to convergence 76 setup time was (sec) 0.3900000 now iterating at: 15:12:07 rms-change max change #iterations 0.1791131 23.16337 at 10iterations 2.0107074E-02 3.016329 at 20iterations 2.2372776E-03 0.2707663 at 30iterations 2.8559470E-04 3.8208008E-02 at 40iterations 5.0077499E-05 5.8135986E-03 at 50iterations finished qdiffx linear iterations at : 15:12:10 total time elapsed so far: 3.350000 # loops : 50 mean,max change (kT/e) : 5.0077499E-05 5.8135986E-03 energy calculations done at 3.350000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.490000 DelPhi exited at 15:12:10 3.494u 0.214s 0:04.07 90.9% 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 Sat Oct 15 2011 at 15:12:10 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2734 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: 2.003452 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): -12.06500 37.46200 ymin,ymax (A): -26.57300 21.47200 zmin,zma (A): -7.925000 45.38300 x,y,z range (A): 49.52700 48.04500 53.30800 scale (grids/A): 2.003452 object centre (A): 12.69850 -2.550500 18.72900 number of atom coordinates read : 2734 total number of charged atoms : 2587 net assigned charge : 7.500018 assigned positive charge : 412.1918 centred at (gu) : 91.10655 91.25081 93.58862 assigned negative charge : -404.6924 centred at (gu) : 90.38380 90.75485 93.91258 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 86454 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22220 grid for indexing accessible points = 1.400000 m= 33091 mr = 61455 m= 5661 mr = 25409 m= 380 mr = 3752 m= 5 mr = 146 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 2540 time to turn everything in is 0.4300000 number of dielectric boundary points 34829 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 145 iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 20489 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) : 0.6678172 object centre at (A) : 12.69850 -2.550500 18.72900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.3848708E-02 7.7286904E-04 midg,1,midg; midg,igrid,midg -1.4587643E-02 4.1317936E-02 1,midg,midg; igrid,midg,midg -3.2108247E-03 8.5957527E-02 gauss-seidel spectral radius is 0.9987683 estimated iterations to convergence 226 setup time was (sec) 0.6700000 now iterating at: 15:12:11 rms-change max change #iterations 4.815980 241.3229 at 10iterations 2.350155 79.57214 at 20iterations 1.148271 35.20759 at 30iterations 0.5604274 16.40718 at 40iterations 0.2734680 8.544350 at 50iterations 0.1331856 3.835970 at 60iterations 6.5091193E-02 1.989352 at 70iterations 3.1835623E-02 0.9571776 at 80iterations 1.5605750E-02 0.4383898 at 90iterations 7.6396717E-03 0.2100382 at 100iterations 3.7921623E-03 0.1233482 at 110iterations 1.9015942E-03 5.4794312E-02 at 120iterations finished qdiffx linear iterations at : 15:12:19 total time elapsed so far: 8.120000 # loops : 120 mean,max change (kT/e) : 1.9015942E-03 5.4794312E-02 energy calculations done at 8.120000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.250000 DelPhi exited at 15:12:19 8.253u 0.210s 0:08.91 94.9% 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 Sat Oct 15 2011 at 15:12:19 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2734 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.005177 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): -12.06500 37.46200 ymin,ymax (A): -26.57300 21.47200 zmin,zma (A): -7.925000 45.38300 x,y,z range (A): 49.52700 48.04500 53.30800 scale (grids/A): 3.005177 object centre (A): 12.69850 -2.550500 18.72900 number of atom coordinates read : 2734 total number of charged atoms : 2587 net assigned charge : 7.500018 assigned positive charge : 412.1918 centred at (gu) : 91.65972 91.87598 95.38291 assigned negative charge : -404.6924 centred at (gu) : 90.57563 91.13219 95.86872 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3800000 boundary points on vw surface= 199461 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22220 grid for indexing accessible points = 1.400000 m= 105639 mr = 148142 m= 40781 mr = 88272 m= 10372 mr = 33865 m= 1599 mr = 8081 m= 103 mr = 1074 m= 3 mr = 41 m= 0 mr = 0 time to grow re-entrant surface = 0.6500000 no. cavity mid-points inaccessible to solvent = 8297 time to turn everything in is 1.130000 number of dielectric boundary points 78483 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.240000 number of grid points assigned charge 20691 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) : 2.003452 object centre at (A) : 12.69850 -2.550500 18.72900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4610134 0.2237877 midg,1,midg; midg,igrid,midg -0.1835364 0.4455545 1,midg,midg; igrid,midg,midg -1.5572858E-02 0.7157405 gauss-seidel spectral radius is 0.9992876 estimated iterations to convergence 296 setup time was (sec) 1.390000 now iterating at: 15:12:21 rms-change max change #iterations 10.95127 410.8798 at 10iterations 6.452433 165.7100 at 20iterations 3.798014 84.46243 at 30iterations 2.228710 46.44603 at 40iterations 1.307572 28.01208 at 50iterations 0.7665564 14.60384 at 60iterations 0.4473338 9.573760 at 70iterations 0.2614253 4.737716 at 80iterations 0.1528730 3.242891 at 90iterations 8.9221805E-02 1.472664 at 100iterations 5.1923312E-02 0.8234699 at 110iterations 3.0294217E-02 0.6267484 at 120iterations 1.7666381E-02 0.2992821 at 130iterations 1.0347603E-02 0.1840219 at 140iterations 6.0539455E-03 0.1230812 at 150iterations 3.5759141E-03 6.6669464E-02 at 160iterations 2.1321564E-03 3.7212372E-02 at 170iterations 1.2940953E-03 2.4566650E-02 at 180iterations finished qdiffx linear iterations at : 15:12:39 total time elapsed so far: 13.44000 # loops : 180 mean,max change (kT/e) : 1.2940953E-03 2.4566650E-02 energy calculations done at 13.44000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.56000 DelPhi exited at 15:12:40 13.564u 0.241s 0:20.76 66.4% 0+0k 0+0io 0pf+0w