Mon Oct 10 22:02:04 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 Mon Oct 10 2011 at 22:02:04 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: 296 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2726 !!! WARNING: ASL 37 has a net charge of -0.1000 !!! WARNING: GLM 43 has a net charge of -0.0940 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: 0.6230530 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): -9.256000 42.76300 ymin,ymax (A): -25.42700 31.71100 zmin,zma (A): -26.19900 24.03600 x,y,z range (A): 52.01900 57.13800 50.23500 scale (grids/A): 0.6230530 object centre (A): 16.75350 3.142000 -1.081500 number of atom coordinates read : 2726 total number of charged atoms : 2634 net assigned charge : 3.806005 assigned positive charge : 414.3843 centred at (gu) : 88.97959 89.38281 90.73445 assigned negative charge : -410.5796 centred at (gu) : 88.86116 89.40173 90.74039 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 7192 nv = 96 ne = 84 npr = 52914 no. pairs analyzed = 52914 no. exposed pairs = 3801 no. arc points = 26506 no. surface atoms = 1264 nbur = 1462 mkacc time = 8.9999996E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 384 mr = 3635 m= 2 mr = 29 m= 0 mr = 0 time to grow re-entrant surface = 9.9999987E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2100000 number of dielectric boundary points 3914 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2647 ## 247 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 8802 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.3479253E-09 3.5079664E-09 midg,1,midg; midg,igrid,midg 5.6072924E-09 1.7693290E-09 1,midg,midg; igrid,midg,midg -7.2759052E-09 9.9320880E-09 gauss-seidel spectral radius is 0.9866807 estimated iterations to convergence 71 setup time was (sec) 0.4000000 now iterating at: 22:02:04 rms-change max change #iterations 0.1307653 21.34100 at 10iterations 1.2080678E-02 1.847624 at 20iterations 1.1717433E-03 0.1745090 at 30iterations 1.4227124E-04 1.8859863E-02 at 40iterations 2.9345767E-05 3.7341118E-03 at 50iterations finished qdiffx linear iterations at : 22:02:07 total time elapsed so far: 3.300000 # loops : 50 mean,max change (kT/e) : 2.9345767E-05 3.7341118E-03 energy calculations done at 3.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.420000 DelPhi exited at 22:02:08 3.428u 0.190s 0:04.31 83.7% 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 22:02:08 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: 296 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2726 !!! WARNING: ASL 37 has a net charge of -0.1000 !!! WARNING: GLM 43 has a net charge of -0.0940 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: 1.869159 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): -9.256000 42.76300 ymin,ymax (A): -25.42700 31.71100 zmin,zma (A): -26.19900 24.03600 x,y,z range (A): 52.01900 57.13800 50.23500 scale (grids/A): 1.869159 object centre (A): 16.75350 3.142000 -1.081500 number of atom coordinates read : 2726 total number of charged atoms : 2634 net assigned charge : 3.806005 assigned positive charge : 414.3843 centred at (gu) : 86.93802 88.14745 92.20263 assigned negative charge : -410.5796 centred at (gu) : 86.58334 88.20506 92.22090 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 77946 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26506 grid for indexing accessible points = 1.400000 m= 26401 mr = 51907 m= 3999 mr = 18128 m= 184 mr = 2352 m= 5 mr = 47 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3900000 number of dielectric boundary points 36101 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 172 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 20613 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) : 0.6230530 object centre at (A) : 16.75350 3.142000 -1.081500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.3377084E-03 5.7449942E-03 midg,1,midg; midg,igrid,midg 1.3030218E-02 1.1749363E-02 1,midg,midg; igrid,midg,midg -1.9187430E-02 1.8875372E-02 gauss-seidel spectral radius is 0.9986176 estimated iterations to convergence 213 setup time was (sec) 0.6200000 now iterating at: 22:02:09 rms-change max change #iterations 4.271304 182.3138 at 10iterations 1.986960 68.04356 at 20iterations 0.9287515 31.76017 at 30iterations 0.4331690 14.56649 at 40iterations 0.2027794 6.286633 at 50iterations 9.4838597E-02 2.999522 at 60iterations 4.4325460E-02 1.597754 at 70iterations 2.0673379E-02 0.7763977 at 80iterations 9.6172336E-03 0.3101578 at 90iterations 4.4941823E-03 0.1379414 at 100iterations 2.0961638E-03 6.5020442E-02 at 110iterations 9.8244415E-04 3.7658691E-02 at 120iterations finished qdiffx linear iterations at : 22:02:16 total time elapsed so far: 7.800000 # loops : 120 mean,max change (kT/e) : 9.8244415E-04 3.7658691E-02 energy calculations done at 7.800000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.940000 DelPhi exited at 22:02:16 7.940u 0.191s 0:08.51 95.5% 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 22:02:17 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: 296 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2726 !!! WARNING: ASL 37 has a net charge of -0.1000 !!! WARNING: GLM 43 has a net charge of -0.0940 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: 2.803738 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): -9.256000 42.76300 ymin,ymax (A): -25.42700 31.71100 zmin,zma (A): -26.19900 24.03600 x,y,z range (A): 52.01900 57.13800 50.23500 scale (grids/A): 2.803738 object centre (A): 16.75350 3.142000 -1.081500 number of atom coordinates read : 2726 total number of charged atoms : 2634 net assigned charge : 3.806005 assigned positive charge : 414.3843 centred at (gu) : 85.40687 87.22104 93.30370 assigned negative charge : -410.5796 centred at (gu) : 84.87505 87.30747 93.33145 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 180387 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26506 grid for indexing accessible points = 1.400000 m= 85611 mr = 126614 m= 29864 mr = 67109 m= 6872 mr = 22937 m= 854 mr = 4924 m= 45 mr = 514 m= 1 mr = 18 m= 0 mr = 0 time to grow re-entrant surface = 0.5500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.9700000 number of dielectric boundary points 81518 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.080000 number of grid points assigned charge 21059 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) : 1.869159 object centre at (A) : 16.75350 3.142000 -1.081500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1619620 6.2405773E-02 midg,1,midg; midg,igrid,midg 1.0798799E-03 8.3831929E-02 1,midg,midg; igrid,midg,midg -0.2814765 0.2069647 gauss-seidel spectral radius is 0.9992761 estimated iterations to convergence 293 setup time was (sec) 1.230000 now iterating at: 22:02:18 rms-change max change #iterations 10.31433 370.6808 at 10iterations 6.178897 153.3800 at 20iterations 3.654403 82.12092 at 30iterations 2.154455 51.48312 at 40iterations 1.263326 29.68439 at 50iterations 0.7376218 15.85260 at 60iterations 0.4298733 9.585078 at 70iterations 0.2507342 5.008698 at 80iterations 0.1457299 3.040062 at 90iterations 8.4543049E-02 1.631249 at 100iterations 4.9062900E-02 0.8882909 at 110iterations 2.8465876E-02 0.5249825 at 120iterations 1.6466323E-02 0.3175907 at 130iterations 9.5537538E-03 0.1653519 at 140iterations 5.5358796E-03 0.1145267 at 150iterations 3.2017962E-03 6.1012268E-02 at 160iterations 1.8548596E-03 3.3699036E-02 at 170iterations 1.0753360E-03 1.9305706E-02 at 180iterations finished qdiffx linear iterations at : 22:02:30 total time elapsed so far: 12.81000 # loops : 180 mean,max change (kT/e) : 1.0753360E-03 1.9305706E-02 energy calculations done at 12.81000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.94000 DelPhi exited at 22:02:30 12.943u 0.207s 0:13.45 97.6% 0+0k 0+0io 0pf+0w