Sat Oct 8 19:18:29 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 8 2011 at 19:18:29 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2602 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN9 901 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.6283424 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): -31.81300 17.69900 ymin,ymax (A): -23.75600 22.90300 zmin,zma (A): -12.33300 44.32400 x,y,z range (A): 49.51200 46.65900 56.65700 scale (grids/A): 0.6283424 object centre (A): -7.057000 -0.4265003 15.99550 number of atom coordinates read : 2602 total number of charged atoms : 2466 net assigned charge : 4.500007 assigned positive charge : 393.3950 centred at (gu) : 88.59174 89.29298 89.83320 assigned negative charge : -388.8955 centred at (gu) : 88.48727 89.33726 89.73026 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6796 nv = 96 ne = 84 npr = 54627 no. pairs analyzed = 54627 no. exposed pairs = 2978 no. arc points = 21565 no. surface atoms = 1005 nbur = 1597 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 338 mr = 3848 m= 4 mr = 49 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 117 time to turn everything in is 0.3000000 number of dielectric boundary points 3241 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2111 ## 196 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 8245 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.1597028E-09 1.2893151E-08 midg,1,midg; midg,igrid,midg 9.9068185E-09 9.1471714E-10 1,midg,midg; igrid,midg,midg -5.7722458E-09 9.9577449E-09 gauss-seidel spectral radius is 0.9868764 estimated iterations to convergence 71 setup time was (sec) 0.5100000 now iterating at: 19:18:30 rms-change max change #iterations 0.1367607 19.07457 at 10iterations 1.3115356E-02 2.240878 at 20iterations 1.2369963E-03 0.1791267 at 30iterations 1.1769870E-04 1.7066002E-02 at 40iterations 1.1345350E-05 1.5907288E-03 at 50iterations finished qdiffx linear iterations at : 19:18:33 total time elapsed so far: 2.990000 # loops : 50 mean,max change (kT/e) : 1.1345350E-05 1.5907288E-03 energy calculations done at 2.990000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.170000 DelPhi exited at 19:18:33 3.175u 0.158s 0:03.61 91.9% 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 8 2011 at 19:18:33 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2602 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN9 901 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.885027 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): -31.81300 17.69900 ymin,ymax (A): -23.75600 22.90300 zmin,zma (A): -12.33300 44.32400 x,y,z range (A): 49.51200 46.65900 56.65700 scale (grids/A): 1.885027 object centre (A): -7.057000 -0.4265003 15.99550 number of atom coordinates read : 2602 total number of charged atoms : 2466 net assigned charge : 4.500007 assigned positive charge : 393.3950 centred at (gu) : 85.77441 87.87898 89.49908 assigned negative charge : -388.8955 centred at (gu) : 85.46146 88.01152 89.19046 start vw surface at 0.1500000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 73278 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21565 grid for indexing accessible points = 1.400000 m= 26578 mr = 51518 m= 4105 mr = 20153 m= 191 mr = 2635 m= 0 mr = 50 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 5265 time to turn everything in is 0.5300000 number of dielectric boundary points 29796 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 164 iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 19383 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) : 0.6283424 object centre at (A) : -7.057000 -0.4265003 15.99550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.2422707E-02 3.1252932E-02 midg,1,midg; midg,igrid,midg 1.6781028E-02 3.4300119E-03 1,midg,midg; igrid,midg,midg -4.6822513E-03 4.1005407E-02 gauss-seidel spectral radius is 0.9986034 estimated iterations to convergence 212 setup time was (sec) 0.8200000 now iterating at: 19:18:34 rms-change max change #iterations 4.150708 194.8327 at 10iterations 1.923296 69.81652 at 20iterations 0.8931828 30.10352 at 30iterations 0.4135580 13.55037 at 40iterations 0.1928350 6.321996 at 50iterations 8.9527316E-02 2.828896 at 60iterations 4.1675281E-02 1.387642 at 70iterations 1.9324316E-02 0.6278343 at 80iterations 8.9822244E-03 0.2767868 at 90iterations 4.1614170E-03 0.1355972 at 100iterations 1.9414313E-03 6.3636780E-02 at 110iterations 9.0128410E-04 3.0148506E-02 at 120iterations finished qdiffx linear iterations at : 19:18:41 total time elapsed so far: 7.290000 # loops : 120 mean,max change (kT/e) : 9.0128410E-04 3.0148506E-02 energy calculations done at 7.290000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.460000 DelPhi exited at 19:18:41 7.467u 0.235s 0:07.98 96.3% 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 8 2011 at 19:18:41 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2602 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN9 901 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.827541 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): -31.81300 17.69900 ymin,ymax (A): -23.75600 22.90300 zmin,zma (A): -12.33300 44.32400 x,y,z range (A): 49.51200 46.65900 56.65700 scale (grids/A): 2.827541 object centre (A): -7.057000 -0.4265003 15.99550 number of atom coordinates read : 2602 total number of charged atoms : 2466 net assigned charge : 4.500007 assigned positive charge : 393.3950 centred at (gu) : 83.66157 86.81837 89.24854 assigned negative charge : -388.8955 centred at (gu) : 83.19226 87.01737 88.78566 start vw surface at 0.1500000 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 169412 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21565 grid for indexing accessible points = 1.400000 m= 86786 mr = 124629 m= 31133 mr = 72235 m= 7220 mr = 25455 m= 934 mr = 5520 m= 41 mr = 623 m= 0 mr = 12 time to grow re-entrant surface = 0.7499999 no. cavity mid-points inaccessible to solvent = 17387 time to turn everything in is 1.310000 number of dielectric boundary points 67052 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.450000 number of grid points assigned charge 19727 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) : 1.885027 object centre at (A) : -7.057000 -0.4265003 15.99550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1633899 0.4074816 midg,1,midg; midg,igrid,midg 0.1933427 2.0910915E-02 1,midg,midg; igrid,midg,midg -5.5239769E-04 0.5170416 gauss-seidel spectral radius is 0.9992439 estimated iterations to convergence 287 setup time was (sec) 1.620000 now iterating at: 19:18:43 rms-change max change #iterations 9.657321 345.3683 at 10iterations 5.563330 105.7766 at 20iterations 3.192394 82.39226 at 30iterations 1.824158 32.19584 at 40iterations 1.043585 20.45160 at 50iterations 0.5952099 11.26273 at 60iterations 0.3403648 6.176590 at 70iterations 0.1944584 3.741112 at 80iterations 0.1110610 2.036888 at 90iterations 6.3287683E-02 1.100473 at 100iterations 3.6215987E-02 0.7181149 at 110iterations 2.0649502E-02 0.3819078 at 120iterations 1.1775604E-02 0.2220306 at 130iterations 6.7175445E-03 0.1242867 at 140iterations 3.8330324E-03 6.8519592E-02 at 150iterations 2.1839822E-03 4.3138504E-02 at 160iterations 1.2489734E-03 2.2916794E-02 at 170iterations 7.1237324E-04 1.3870239E-02 at 180iterations finished qdiffx linear iterations at : 19:18:53 total time elapsed so far: 11.86000 # loops : 180 mean,max change (kT/e) : 7.1237324E-04 1.3870239E-02 energy calculations done at 11.86000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.02000 DelPhi exited at 19:18:54 12.026u 0.240s 0:12.62 97.1% 0+0k 0+0io 0pf+0w