Thu Jan 19 13:33:51 PST 2012 #!/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 Thu Jan 19 2012 at 13:33:51 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: 416 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 6864 !!! WARNING: ARG 48 has a net charge of 0.0400 !!! WARNING: ARG 52 has a net charge of 0.0400 !!! WARNING: HIR 59 has a net charge of 0.5220 !!! WARNING: LYS 138 has a net charge of 0.0200 !!! WARNING: GLN 139 has a net charge of 0.0170 !!! WARNING: ASP 142 has a net charge of -0.2080 !!! WARNING: LYS 155 has a net charge of 0.0200 !!! WARNING: GLM 161 has a net charge of -0.0940 !!! WARNING: LYS 184 has a net charge of 0.0200 !!! WARNING: LYS 286 has a net charge of 0.0200 !!! WARNING: HIZ 357 has a net charge of 0.2000 !!! WARNING: ARG 365 has a net charge of 0.0400 !!! WARNING: GLN 369 has a net charge of 0.0170 !!! WARNING: ASP 385 has a net charge of -0.2080 !!! WARNING: LYS 442 has a net charge of 0.0200 !!! WARNING: GLN 448 has a net charge of 0.0170 !!! WARNING: LYS 454 has a net charge of 0.0200 !!! WARNING: ARG 601 has a net charge of 0.0400 !!! WARNING: HEM 1107 has a net charge of -4.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 0.4370512 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): -3.559000 62.58600 ymin,ymax (A): 17.63500 94.08400 zmin,zma (A): -15.55900 65.89600 x,y,z range (A): 66.14500 76.44900 81.45499 scale (grids/A): 0.4370512 object centre (A): 29.51350 55.85950 25.16850 number of atom coordinates read : 6864 total number of charged atoms : 6691 net assigned charge : -1.456947 assigned positive charge : 1038.335 centred at (gu) : 88.99688 90.00941 88.34216 assigned negative charge : -1039.801 centred at (gu) : 88.97462 90.01823 88.32981 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 7847 nv = 96 ne = 84 npr = 138238 no. pairs analyzed = 138238 no. exposed pairs = 8919 no. arc points = 60927 no. surface atoms = 3015 nbur = 3849 mkacc time = 0.2400000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.904000 m= 223 mr = 3735 m= 0 mr = 2 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4500000 number of dielectric boundary points 4333 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5072 ## 976 charges are in solution ## iepsmp to db, and charging done at 0.5400000 number of grid points assigned charge 10796 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.6483444E-12 4.5851940E-13 midg,1,midg; midg,igrid,midg 4.3313183E-13 -1.2538176E-12 1,midg,midg; igrid,midg,midg -3.4604906E-12 1.2539670E-12 gauss-seidel spectral radius is 0.9734378 estimated iterations to convergence 51 setup time was (sec) 0.6700000 now iterating at: 13:33:52 rms-change max change #iterations 3.4861997E-02 5.357903 at 10iterations 2.6865844E-03 0.4382935 at 20iterations 9.5781259E-04 0.1574745 at 30iterations 3.7827430E-04 6.0770035E-02 at 40iterations 1.4879195E-04 2.3555756E-02 at 50iterations finished qdiffx linear iterations at : 13:33:58 total time elapsed so far: 3.820000 # loops : 50 mean,max change (kT/e) : 1.4879195E-04 2.3555756E-02 energy calculations done at 3.820000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.970000 DelPhi exited at 13:33:58 3.972u 0.209s 0:07.61 54.7% 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 Thu Jan 19 2012 at 13:33:59 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: 416 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 6864 !!! WARNING: ARG 48 has a net charge of 0.0400 !!! WARNING: ARG 52 has a net charge of 0.0400 !!! WARNING: HIR 59 has a net charge of 0.5220 !!! WARNING: LYS 138 has a net charge of 0.0200 !!! WARNING: GLN 139 has a net charge of 0.0170 !!! WARNING: ASP 142 has a net charge of -0.2080 !!! WARNING: LYS 155 has a net charge of 0.0200 !!! WARNING: GLM 161 has a net charge of -0.0940 !!! WARNING: LYS 184 has a net charge of 0.0200 !!! WARNING: LYS 286 has a net charge of 0.0200 !!! WARNING: HIZ 357 has a net charge of 0.2000 !!! WARNING: ARG 365 has a net charge of 0.0400 !!! WARNING: GLN 369 has a net charge of 0.0170 !!! WARNING: ASP 385 has a net charge of -0.2080 !!! WARNING: LYS 442 has a net charge of 0.0200 !!! WARNING: GLN 448 has a net charge of 0.0170 !!! WARNING: LYS 454 has a net charge of 0.0200 !!! WARNING: ARG 601 has a net charge of 0.0400 !!! WARNING: HEM 1107 has a net charge of -4.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 1.311154 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): -3.559000 62.58600 ymin,ymax (A): 17.63500 94.08400 zmin,zma (A): -15.55900 65.89600 x,y,z range (A): 66.14500 76.44900 81.45499 scale (grids/A): 1.311154 object centre (A): 29.51350 55.85950 25.16850 number of atom coordinates read : 6864 total number of charged atoms : 6691 net assigned charge : -1.456947 assigned positive charge : 1038.335 centred at (gu) : 86.98847 90.02641 85.02470 assigned negative charge : -1039.801 centred at (gu) : 86.92382 90.05442 84.98946 start vw surface at 0.1800000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 91475 reading accessible surface arcs data from file ARCDAT no. of arc points read = 60927 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.792000 m= 21968 mr = 60400 m= 1177 mr = 13143 m= 10 mr = 292 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 454 time to turn everything in is 0.5100000 number of dielectric boundary points 40795 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1001 ## 30 charges are in solution ## iepsmp to db, and charging done at 0.6000000 number of grid points assigned charge 46897 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) : 0.4370512 object centre at (A) : 29.51350 55.85950 25.16850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.7093992E-03 1.1694890E-03 midg,1,midg; midg,igrid,midg -2.0344374E-03 3.2938810E-03 1,midg,midg; igrid,midg,midg -7.5836643E-04 1.8721869E-03 gauss-seidel spectral radius is 0.9975144 estimated iterations to convergence 160 setup time was (sec) 0.7400000 now iterating at: 13:34:00 rms-change max change #iterations 3.233788 149.1836 at 10iterations 1.157290 38.30793 at 20iterations 0.4172431 14.06729 at 30iterations 0.1505484 5.868637 at 40iterations 5.4532550E-02 2.202125 at 50iterations 1.9853631E-02 0.6468353 at 60iterations 7.4755596E-03 0.2846985 at 70iterations 3.1067717E-03 0.1111927 at 80iterations 1.5568209E-03 5.5913925E-02 at 90iterations 9.4765914E-04 3.3058167E-02 at 100iterations 6.3537445E-04 2.0437241E-02 at 110iterations 4.4003714E-04 1.3885498E-02 at 120iterations finished qdiffx linear iterations at : 13:34:14 total time elapsed so far: 8.370000 # loops : 120 mean,max change (kT/e) : 4.4003714E-04 1.3885498E-02 energy calculations done at 8.370000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.510000 DelPhi exited at 13:34:15 8.515u 0.232s 0:16.10 54.2% 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 Thu Jan 19 2012 at 13:34:15 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: 416 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 6864 !!! WARNING: ARG 48 has a net charge of 0.0400 !!! WARNING: ARG 52 has a net charge of 0.0400 !!! WARNING: HIR 59 has a net charge of 0.5220 !!! WARNING: LYS 138 has a net charge of 0.0200 !!! WARNING: GLN 139 has a net charge of 0.0170 !!! WARNING: ASP 142 has a net charge of -0.2080 !!! WARNING: LYS 155 has a net charge of 0.0200 !!! WARNING: GLM 161 has a net charge of -0.0940 !!! WARNING: LYS 184 has a net charge of 0.0200 !!! WARNING: LYS 286 has a net charge of 0.0200 !!! WARNING: HIZ 357 has a net charge of 0.2000 !!! WARNING: ARG 365 has a net charge of 0.0400 !!! WARNING: GLN 369 has a net charge of 0.0170 !!! WARNING: ASP 385 has a net charge of -0.2080 !!! WARNING: LYS 442 has a net charge of 0.0200 !!! WARNING: GLN 448 has a net charge of 0.0170 !!! WARNING: LYS 454 has a net charge of 0.0200 !!! WARNING: ARG 601 has a net charge of 0.0400 !!! WARNING: HEM 1107 has a net charge of -4.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 1.966730 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): -3.559000 62.58600 ymin,ymax (A): 17.63500 94.08400 zmin,zma (A): -15.55900 65.89600 x,y,z range (A): 66.14500 76.44900 81.45499 scale (grids/A): 1.966730 object centre (A): 29.51350 55.85950 25.16850 number of atom coordinates read : 6864 total number of charged atoms : 6691 net assigned charge : -1.456947 assigned positive charge : 1038.335 centred at (gu) : 85.48234 90.03900 82.53660 assigned negative charge : -1039.801 centred at (gu) : 85.38573 90.08147 82.48384 start vw surface at 0.1800000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 214948 reading accessible surface arcs data from file ARCDAT no. of arc points read = 60927 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.764000 m= 84625 mr = 151216 m= 15799 mr = 62533 m= 1226 mr = 10078 m= 30 mr = 520 m= 0 mr = 0 time to grow re-entrant surface = 0.6200000 no. cavity mid-points inaccessible to solvent = 1423 time to turn everything in is 1.130000 number of dielectric boundary points 92281 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 236 iepsmp to db, and charging done at 1.240000 number of grid points assigned charge 52848 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) : 1.311154 object centre at (A) : 29.51350 55.85950 25.16850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5474038 6.8027087E-02 midg,1,midg; midg,igrid,midg -6.3152276E-02 0.1207713 1,midg,midg; igrid,midg,midg 1.2721426E-03 4.5978677E-02 gauss-seidel spectral radius is 0.9990188 estimated iterations to convergence 252 setup time was (sec) 1.410000 now iterating at: 13:34:16 rms-change max change #iterations 9.840520 280.6849 at 10iterations 5.425656 136.8374 at 20iterations 2.947047 80.74873 at 30iterations 1.593971 35.18711 at 40iterations 0.8566735 18.10204 at 50iterations 0.4597744 12.40912 at 60iterations 0.2449288 5.017795 at 70iterations 0.1308138 2.843256 at 80iterations 6.9579326E-02 1.572922 at 90iterations 3.7031196E-02 0.7463903 at 100iterations 1.9685872E-02 0.4336395 at 110iterations 1.0452260E-02 0.2417107 at 120iterations 5.5618859E-03 0.1066837 at 130iterations 2.9714231E-03 5.7547569E-02 at 140iterations 1.5968467E-03 3.4605026E-02 at 150iterations 8.7418698E-04 1.7429352E-02 at 160iterations 4.9186801E-04 1.0116577E-02 at 170iterations 2.9083592E-04 6.0997009E-03 at 180iterations finished qdiffx linear iterations at : 13:34:38 total time elapsed so far: 14.67000 # loops : 180 mean,max change (kT/e) : 2.9083592E-04 6.0997009E-03 energy calculations done at 14.67000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.82000 DelPhi exited at 13:34:38 14.823u 0.270s 0:23.75 63.5% 0+0k 0+0io 0pf+0w