Wed Dec 21 14:20:51 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+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 Wed Dec 21 2011 at 14:20:51 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1913 !!! WARNING: LYS 7 has a net charge of 0.0200 !!! WARNING: LYS 14 has a net charge of 0.0730 !!! WARNING: ARG 41 has a net charge of -0.0090 !!! WARNING: LYS 70 has a net charge of 0.0730 !!! WARNING: LYS 106 has a net charge of 0.1210 !!! WARNING: GLN 117 has a net charge of 0.0170 !!! WARNING: LYS 154 has a net charge of 0.0730 !!! WARNING: LYS 169 has a net charge of 0.1210 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: 0.6432844 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): -4.688000 35.27500 ymin,ymax (A): -3.644000 47.27800 zmin,zma (A): -24.28500 31.05600 x,y,z range (A): 39.96300 50.92200 55.34100 scale (grids/A): 0.6432844 object centre (A): 15.29350 21.81700 3.385500 number of atom coordinates read : 1913 total number of charged atoms : 1781 net assigned charge : -2.510996 assigned positive charge : 276.2172 centred at (gu) : 90.42569 92.91721 90.09420 assigned negative charge : -278.7283 centred at (gu) : 90.54912 93.11035 90.09611 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 5520 nv = 96 ne = 84 npr = 39612 no. pairs analyzed = 39612 no. exposed pairs = 2406 no. arc points = 16695 no. surface atoms = 818 nbur = 1095 mkacc time = 7.0000008E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 292 mr = 3127 m= 0 mr = 54 time to grow re-entrant surface = 8.0000013E-02 no. cavity mid-points inaccessible to solvent = 29 time to turn everything in is 0.1700000 number of dielectric boundary points 2631 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1643 ## 162 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 6352 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.0914145E-09 -3.5638457E-09 midg,1,midg; midg,igrid,midg 7.3391928E-09 -4.0155044E-08 1,midg,midg; igrid,midg,midg 7.0063417E-09 -1.6050979E-08 gauss-seidel spectral radius is 0.9874195 estimated iterations to convergence 73 setup time was (sec) 0.4300000 now iterating at: 14:20:52 rms-change max change #iterations 0.1209796 17.86270 at 10iterations 1.2261371E-02 2.293163 at 20iterations 1.2170698E-03 0.2149076 at 30iterations 1.2246879E-04 1.9281864E-02 at 40iterations 1.2244945E-05 2.3021698E-03 at 50iterations finished qdiffx linear iterations at : 14:20:56 total time elapsed so far: 3.900000 # loops : 50 mean,max change (kT/e) : 1.2244945E-05 2.3021698E-03 energy calculations done at 3.900000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.030000 DelPhi exited at 14:20:56 4.029u 0.412s 0:04.83 91.7% 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 Wed Dec 21 2011 at 14:20:56 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 = 1913 !!! WARNING: LYS 7 has a net charge of 0.0200 !!! WARNING: LYS 14 has a net charge of 0.0730 !!! WARNING: ARG 41 has a net charge of -0.0090 !!! WARNING: LYS 70 has a net charge of 0.0730 !!! WARNING: LYS 106 has a net charge of 0.1210 !!! WARNING: GLN 117 has a net charge of 0.0170 !!! WARNING: LYS 154 has a net charge of 0.0730 !!! WARNING: LYS 169 has a net charge of 0.1210 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: 1.929853 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): -4.688000 35.27500 ymin,ymax (A): -3.644000 47.27800 zmin,zma (A): -24.28500 31.05600 x,y,z range (A): 39.96300 50.92200 55.34100 scale (grids/A): 1.929853 object centre (A): 15.29350 21.81700 3.385500 number of atom coordinates read : 1913 total number of charged atoms : 1781 net assigned charge : -2.510996 assigned positive charge : 276.2172 centred at (gu) : 91.27724 98.75148 90.28289 assigned negative charge : -278.7283 centred at (gu) : 91.64750 99.33107 90.28831 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 58965 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16695 grid for indexing accessible points = 1.400000 m= 22920 mr = 41036 m= 3797 mr = 17842 m= 246 mr = 2526 m= 2 mr = 125 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 1496 time to turn everything in is 0.3700000 number of dielectric boundary points 24401 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 103 iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 14046 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) : 0.6432844 object centre at (A) : 15.29350 21.81700 3.385500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.5258870E-02 2.3553453E-03 midg,1,midg; midg,igrid,midg 1.9116979E-02 -3.2661796E-02 1,midg,midg; igrid,midg,midg 2.8427886E-03 -8.6217485E-03 gauss-seidel spectral radius is 0.9985865 estimated iterations to convergence 211 setup time was (sec) 0.7500000 now iterating at: 14:20:57 rms-change max change #iterations 3.582973 163.1482 at 10iterations 1.653453 60.43588 at 20iterations 0.7669513 29.22176 at 30iterations 0.3545606 12.71051 at 40iterations 0.1639631 6.393894 at 50iterations 7.5426936E-02 3.402235 at 60iterations 3.4834806E-02 1.366583 at 70iterations 1.6086824E-02 0.5571117 at 80iterations 7.4492502E-03 0.2576447 at 90iterations 3.4406821E-03 0.1189384 at 100iterations 1.5890407E-03 5.4080248E-02 at 110iterations 7.3710200E-04 2.7557373E-02 at 120iterations finished qdiffx linear iterations at : 14:21:06 total time elapsed so far: 9.720000 # loops : 120 mean,max change (kT/e) : 7.3710200E-04 2.7557373E-02 energy calculations done at 9.720000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.850000 DelPhi exited at 14:21:08 9.856u 0.431s 0:12.00 85.6% 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 14:21:08 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1913 !!! WARNING: LYS 7 has a net charge of 0.0200 !!! WARNING: LYS 14 has a net charge of 0.0730 !!! WARNING: ARG 41 has a net charge of -0.0090 !!! WARNING: LYS 70 has a net charge of 0.0730 !!! WARNING: LYS 106 has a net charge of 0.1210 !!! WARNING: GLN 117 has a net charge of 0.0170 !!! WARNING: LYS 154 has a net charge of 0.0730 !!! WARNING: LYS 169 has a net charge of 0.1210 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: 2.894780 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): -4.688000 35.27500 ymin,ymax (A): -3.644000 47.27800 zmin,zma (A): -24.28500 31.05600 x,y,z range (A): 39.96300 50.92200 55.34100 scale (grids/A): 2.894780 object centre (A): 15.29350 21.81700 3.385500 number of atom coordinates read : 1913 total number of charged atoms : 1781 net assigned charge : -2.510996 assigned positive charge : 276.2172 centred at (gu) : 91.91585 103.1273 90.42451 assigned negative charge : -278.7283 centred at (gu) : 92.47134 103.9967 90.43259 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 136095 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16695 grid for indexing accessible points = 1.400000 m= 72212 mr = 98852 m= 28440 mr = 60714 m= 6885 mr = 23928 m= 1001 mr = 5394 m= 87 mr = 763 m= 2 mr = 56 m= 0 mr = 0 time to grow re-entrant surface = 0.4900000 no. cavity mid-points inaccessible to solvent = 5259 time to turn everything in is 0.9500000 number of dielectric boundary points 55015 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.110000 number of grid points assigned charge 14248 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) : 1.929853 object centre at (A) : 15.29350 21.81700 3.385500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.6703461 -3.1171793E-02 midg,1,midg; midg,igrid,midg 0.1560337 -0.2843553 1,midg,midg; igrid,midg,midg 1.0292067E-02 -5.4334637E-02 gauss-seidel spectral radius is 0.9992310 estimated iterations to convergence 285 setup time was (sec) 1.360000 now iterating at: 14:21:10 rms-change max change #iterations 8.470680 535.7646 at 10iterations 4.859606 139.2132 at 20iterations 2.771188 65.05240 at 30iterations 1.570574 34.89256 at 40iterations 0.8949711 22.75993 at 50iterations 0.5081798 10.21408 at 60iterations 0.2889476 6.013855 at 70iterations 0.1641884 3.357056 at 80iterations 9.2845090E-02 1.815048 at 90iterations 5.2810438E-02 1.085251 at 100iterations 2.9967031E-02 0.5916061 at 110iterations 1.7002860E-02 0.3747759 at 120iterations 9.6589224E-03 0.1897960 at 130iterations 5.4609412E-03 0.1109228 at 140iterations 3.1036397E-03 6.4182281E-02 at 150iterations 1.7608006E-03 3.6128998E-02 at 160iterations 1.0010429E-03 2.0366669E-02 at 170iterations 5.6816946E-04 1.2519836E-02 at 180iterations finished qdiffx linear iterations at : 14:21:25 total time elapsed so far: 16.01000 # loops : 180 mean,max change (kT/e) : 5.6816946E-04 1.2519836E-02 energy calculations done at 16.01000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.15000 DelPhi exited at 14:21:34 16.152u 0.519s 0:25.59 65.1% 0+0k 0+0io 0pf+0w