Wed Dec 21 14:21:34 PST 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 Wed Dec 21 2011 at 14:21:35 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: 257 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1895 !!! WARNING: ARG 14 has a net charge of 0.0400 !!! WARNING: LYS 20 has a net charge of 0.0200 !!! WARNING: LYS 41 has a net charge of 0.0200 !!! WARNING: LYS 43 has a net charge of 0.0200 !!! WARNING: LYS 106 has a net charge of 0.0200 !!! WARNING: LYS 140 has a net charge of 0.0200 !!! WARNING: LYS 142 has a net charge of 0.0200 !!! WARNING: LYS 144 has a net charge of 0.0200 !!! WARNING: LYS 169 has a net charge of 0.0200 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: 0.6122519 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): -9.025000 49.12100 ymin,ymax (A): 8.556001 47.80500 zmin,zma (A): -3.603000 38.92000 x,y,z range (A): 58.14600 39.24900 42.52300 scale (grids/A): 0.6122519 object centre (A): 20.04800 28.18050 17.65850 number of atom coordinates read : 1895 total number of charged atoms : 1763 net assigned charge : -3.799991 assigned positive charge : 279.1900 centred at (gu) : 90.26099 89.74609 90.48369 assigned negative charge : -282.9902 centred at (gu) : 90.27792 89.66911 90.57663 start vw surface at 7.9999998E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 4857 nv = 96 ne = 84 npr = 38747 no. pairs analyzed = 38747 no. exposed pairs = 2371 no. arc points = 16481 no. surface atoms = 808 nbur = 1087 mkacc time = 7.0000008E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 212 mr = 2685 m= 0 mr = 12 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 11 time to turn everything in is 0.1600000 number of dielectric boundary points 2372 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1637 ## 164 charges are in solution ## iepsmp to db, and charging done at 0.2300000 number of grid points assigned charge 5804 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0416269E-09 -6.6850383E-09 midg,1,midg; midg,igrid,midg -5.6850675E-09 5.3290716E-10 1,midg,midg; igrid,midg,midg -1.6306543E-09 -3.2067804E-09 gauss-seidel spectral radius is 0.9861296 estimated iterations to convergence 70 setup time was (sec) 0.3500000 now iterating at: 14:21:37 rms-change max change #iterations 0.1052156 22.20622 at 10iterations 9.1811046E-03 1.752306 at 20iterations 8.4760226E-04 0.1427338 at 30iterations 7.2728166E-05 1.2741089E-02 at 40iterations 6.5110526E-06 1.0290146E-03 at 50iterations finished qdiffx linear iterations at : 14:21:40 total time elapsed so far: 3.480000 # loops : 50 mean,max change (kT/e) : 6.5110526E-06 1.0290146E-03 energy calculations done at 3.480000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.620000 DelPhi exited at 14:21:50 3.619u 0.228s 0:15.68 24.4% 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 Wed Dec 21 2011 at 14:21:57 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: 257 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1895 !!! WARNING: ARG 14 has a net charge of 0.0400 !!! WARNING: LYS 20 has a net charge of 0.0200 !!! WARNING: LYS 41 has a net charge of 0.0200 !!! WARNING: LYS 43 has a net charge of 0.0200 !!! WARNING: LYS 106 has a net charge of 0.0200 !!! WARNING: LYS 140 has a net charge of 0.0200 !!! WARNING: LYS 142 has a net charge of 0.0200 !!! WARNING: LYS 144 has a net charge of 0.0200 !!! WARNING: LYS 169 has a net charge of 0.0200 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: 1.836756 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): -9.025000 49.12100 ymin,ymax (A): 8.556001 47.80500 zmin,zma (A): -3.603000 38.92000 x,y,z range (A): 58.14600 39.24900 42.52300 scale (grids/A): 1.836756 object centre (A): 20.04800 28.18050 17.65850 number of atom coordinates read : 1895 total number of charged atoms : 1763 net assigned charge : -3.799991 assigned positive charge : 279.1900 centred at (gu) : 90.78287 89.23815 91.45106 assigned negative charge : -282.9902 centred at (gu) : 90.83402 89.00764 91.72997 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 52994 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16481 grid for indexing accessible points = 1.400000 m= 17961 mr = 36629 m= 2181 mr = 13320 m= 84 mr = 1271 m= 4 mr = 18 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 1491 time to turn everything in is 0.2700000 number of dielectric boundary points 21986 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 97 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.3500000 number of grid points assigned charge 13836 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) : 0.6122519 object centre at (A) : 20.04800 28.18050 17.65850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.5779908E-03 -1.3318685E-02 midg,1,midg; midg,igrid,midg -2.7369338E-03 1.0660399E-03 1,midg,midg; igrid,midg,midg 9.8021957E-04 1.5085853E-02 gauss-seidel spectral radius is 0.9984522 estimated iterations to convergence 202 setup time was (sec) 0.4800000 now iterating at: 14:21:59 rms-change max change #iterations 3.337170 156.3469 at 10iterations 1.479807 60.74572 at 20iterations 0.6583439 23.58590 at 30iterations 0.2944149 11.70458 at 40iterations 0.1314325 4.789483 at 50iterations 5.8423232E-02 2.135365 at 60iterations 2.5943302E-02 1.058846 at 70iterations 1.1623281E-02 0.4482880 at 80iterations 5.1986529E-03 0.2000961 at 90iterations 2.3127689E-03 8.2859039E-02 at 100iterations 1.0292886E-03 3.7567139E-02 at 110iterations 4.5980417E-04 1.8024445E-02 at 120iterations finished qdiffx linear iterations at : 14:22:07 total time elapsed so far: 8.680000 # loops : 120 mean,max change (kT/e) : 4.5980417E-04 1.8024445E-02 energy calculations done at 8.680000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.830000 DelPhi exited at 14:22:17 8.831u 0.230s 0:21.27 42.5% 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 Wed Dec 21 2011 at 14:22:23 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: 257 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1895 !!! WARNING: ARG 14 has a net charge of 0.0400 !!! WARNING: LYS 20 has a net charge of 0.0200 !!! WARNING: LYS 41 has a net charge of 0.0200 !!! WARNING: LYS 43 has a net charge of 0.0200 !!! WARNING: LYS 106 has a net charge of 0.0200 !!! WARNING: LYS 140 has a net charge of 0.0200 !!! WARNING: LYS 142 has a net charge of 0.0200 !!! WARNING: LYS 144 has a net charge of 0.0200 !!! WARNING: LYS 169 has a net charge of 0.0200 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: 2.755133 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): -9.025000 49.12100 ymin,ymax (A): 8.556001 47.80500 zmin,zma (A): -3.603000 38.92000 x,y,z range (A): 58.14600 39.24900 42.52300 scale (grids/A): 2.755133 object centre (A): 20.04800 28.18050 17.65850 number of atom coordinates read : 1895 total number of charged atoms : 1763 net assigned charge : -3.799991 assigned positive charge : 279.1900 centred at (gu) : 91.17441 88.85716 92.17667 assigned negative charge : -282.9902 centred at (gu) : 91.25114 88.51144 92.59504 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 122669 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16481 grid for indexing accessible points = 1.400000 m= 60063 mr = 88752 m= 19472 mr = 49454 m= 3738 mr = 15676 m= 361 mr = 2648 m= 18 mr = 201 m= 1 mr = 1 m= 0 mr = 0 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 5032 time to turn everything in is 0.6700000 number of dielectric boundary points 49590 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 0.7500000 number of grid points assigned charge 14103 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) : 1.836756 object centre at (A) : 20.04800 28.18050 17.65850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.7861133E-03 -0.1328928 midg,1,midg; midg,igrid,midg 8.2782777E-03 1.3547552E-02 1,midg,midg; igrid,midg,midg 7.1235545E-02 0.2689506 gauss-seidel spectral radius is 0.9991884 estimated iterations to convergence 277 setup time was (sec) 0.9000000 now iterating at: 14:22:26 rms-change max change #iterations 7.987364 287.2870 at 10iterations 4.529400 117.5208 at 20iterations 2.552865 70.31682 at 30iterations 1.433052 33.07598 at 40iterations 0.8034141 18.89842 at 50iterations 0.4493218 10.06054 at 60iterations 0.2513990 5.914742 at 70iterations 0.1404458 3.236511 at 80iterations 7.8506768E-02 1.886127 at 90iterations 4.3921836E-02 0.9967117 at 100iterations 2.4501542E-02 0.5214119 at 110iterations 1.3686113E-02 0.2964315 at 120iterations 7.6690875E-03 0.1589279 at 130iterations 4.2715212E-03 9.4745696E-02 at 140iterations 2.3881420E-03 5.1092148E-02 at 150iterations 1.3349801E-03 2.6680946E-02 at 160iterations 7.4422290E-04 1.4941931E-02 at 170iterations 4.1648932E-04 8.5906982E-03 at 180iterations finished qdiffx linear iterations at : 14:22:38 total time elapsed so far: 12.82000 # loops : 180 mean,max change (kT/e) : 4.1648932E-04 8.5906982E-03 energy calculations done at 12.82000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.96000 DelPhi exited at 14:22:42 12.965u 0.228s 0:18.66 70.6% 0+0k 0+0io 0pf+0w