Sat Oct 8 19:44:12 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 Sat Oct 8 2011 at 19:44:12 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2596 !!! WARNING: GLM 92 has a net charge of -0.0940 !!! 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: ZN4 451 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: 0.6259891 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): -32.06000 17.46400 ymin,ymax (A): -23.24600 22.81600 zmin,zma (A): -12.46700 44.40300 x,y,z range (A): 49.52400 46.06200 56.87000 scale (grids/A): 0.6259891 object centre (A): -7.297998 -0.2150002 15.96800 number of atom coordinates read : 2596 total number of charged atoms : 2453 net assigned charge : 4.906007 assigned positive charge : 392.6040 centred at (gu) : 88.60441 89.14242 89.94527 assigned negative charge : -387.6986 centred at (gu) : 88.50568 89.19868 89.81020 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6636 nv = 96 ne = 84 npr = 54594 no. pairs analyzed = 54594 no. exposed pairs = 2957 no. arc points = 21058 no. surface atoms = 996 nbur = 1600 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 326 mr = 3786 m= 3 mr = 39 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 153 time to turn everything in is 0.3000000 number of dielectric boundary points 3140 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2080 ## 202 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 8123 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.0413776E-09 1.5105737E-08 midg,1,midg; midg,igrid,midg 1.1111034E-08 3.4411496E-10 1,midg,midg; igrid,midg,midg -4.2563340E-09 9.2450181E-09 gauss-seidel spectral radius is 0.9867760 estimated iterations to convergence 71 setup time was (sec) 0.5200000 now iterating at: 19:44:13 rms-change max change #iterations 0.1338985 18.07721 at 10iterations 1.2911568E-02 2.102165 at 20iterations 1.2366567E-03 0.1857185 at 30iterations 1.1681647E-04 1.9390106E-02 at 40iterations 1.1251174E-05 1.4452934E-03 at 50iterations finished qdiffx linear iterations at : 19:44:15 total time elapsed so far: 2.950000 # loops : 50 mean,max change (kT/e) : 1.1251174E-05 1.4452934E-03 energy calculations done at 2.950000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.120000 DelPhi exited at 19:44:16 3.123u 0.155s 0:03.54 92.3% 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 19:44:16 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2596 !!! WARNING: GLM 92 has a net charge of -0.0940 !!! 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: ZN4 451 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= 0.1100000 grid size : 179 scale,in grids/A, set to be: 1.877967 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): -32.06000 17.46400 ymin,ymax (A): -23.24600 22.81600 zmin,zma (A): -12.46700 44.40300 x,y,z range (A): 49.52400 46.06200 56.87000 scale (grids/A): 1.877967 object centre (A): -7.297998 -0.2150002 15.96800 number of atom coordinates read : 2596 total number of charged atoms : 2453 net assigned charge : 4.906007 assigned positive charge : 392.6040 centred at (gu) : 85.81252 87.42692 89.83546 assigned negative charge : -387.6986 centred at (gu) : 85.51684 87.59586 89.43041 start vw surface at 0.1800000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 72165 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21058 grid for indexing accessible points = 1.400000 m= 25509 mr = 51154 m= 3590 mr = 19065 m= 164 mr = 2225 m= 2 mr = 52 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 4950 time to turn everything in is 0.5300000 number of dielectric boundary points 28934 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 146 iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 19206 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) : 0.6259891 object centre at (A) : -7.297998 -0.2150002 15.96800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.0982366E-02 3.8654163E-02 midg,1,midg; midg,igrid,midg 1.9770991E-02 2.1219531E-03 1,midg,midg; igrid,midg,midg -3.2614677E-03 3.5260472E-02 gauss-seidel spectral radius is 0.9985896 estimated iterations to convergence 211 setup time was (sec) 0.8000000 now iterating at: 19:44:17 rms-change max change #iterations 4.134926 220.5818 at 10iterations 1.911459 68.24258 at 20iterations 0.8861675 28.43049 at 30iterations 0.4078557 13.56683 at 40iterations 0.1893908 6.124205 at 50iterations 8.7684758E-02 2.855106 at 60iterations 4.0594276E-02 1.325654 at 70iterations 1.8835492E-02 0.6195297 at 80iterations 8.6779129E-03 0.2711573 at 90iterations 4.0237838E-03 0.1250992 at 100iterations 1.8641737E-03 6.2021255E-02 at 110iterations 8.6034473E-04 2.4996758E-02 at 120iterations finished qdiffx linear iterations at : 19:44:23 total time elapsed so far: 6.760000 # loops : 120 mean,max change (kT/e) : 8.6034473E-04 2.4996758E-02 energy calculations done at 6.760000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.930000 DelPhi exited at 19:44:23 6.928u 0.179s 0:07.42 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 Sat Oct 8 2011 at 19:44:23 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2596 !!! WARNING: GLM 92 has a net charge of -0.0940 !!! 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: ZN4 451 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: 2.816951 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): -32.06000 17.46400 ymin,ymax (A): -23.24600 22.81600 zmin,zma (A): -12.46700 44.40300 x,y,z range (A): 49.52400 46.06200 56.87000 scale (grids/A): 2.816951 object centre (A): -7.297998 -0.2150002 15.96800 number of atom coordinates read : 2596 total number of charged atoms : 2453 net assigned charge : 4.906007 assigned positive charge : 392.6040 centred at (gu) : 83.71880 86.14011 89.75307 assigned negative charge : -387.6986 centred at (gu) : 83.27525 86.39357 89.14557 start vw surface at 0.1400000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 167020 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21058 grid for indexing accessible points = 1.400000 m= 84231 mr = 123370 m= 28943 mr = 69852 m= 6284 mr = 23427 m= 730 mr = 4745 m= 31 mr = 477 m= 0 mr = 11 time to grow re-entrant surface = 0.6900001 no. cavity mid-points inaccessible to solvent = 17426 time to turn everything in is 1.210000 number of dielectric boundary points 65357 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.340000 number of grid points assigned charge 19618 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) : 1.877967 object centre at (A) : -7.297998 -0.2150002 15.96800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1097213 0.4597154 midg,1,midg; midg,igrid,midg 0.2211165 1.1984510E-02 1,midg,midg; igrid,midg,midg -6.8524503E-03 0.4387664 gauss-seidel spectral radius is 0.9992373 estimated iterations to convergence 286 setup time was (sec) 1.500000 now iterating at: 19:44:25 rms-change max change #iterations 9.626521 572.8988 at 10iterations 5.538871 135.0461 at 20iterations 3.164902 70.56093 at 30iterations 1.807380 36.66925 at 40iterations 1.032928 20.10883 at 50iterations 0.5878815 10.70498 at 60iterations 0.3360139 6.626001 at 70iterations 0.1915145 3.554283 at 80iterations 0.1091197 2.013540 at 90iterations 6.2228236E-02 1.265192 at 100iterations 3.5375930E-02 0.6324959 at 110iterations 2.0158766E-02 0.3531966 at 120iterations 1.1478969E-02 0.2383728 at 130iterations 6.5545924E-03 0.1211605 at 140iterations 3.7300424E-03 7.8855515E-02 at 150iterations 2.1294057E-03 4.2344093E-02 at 160iterations 1.2161606E-03 2.4154663E-02 at 170iterations 6.9569011E-04 1.3378143E-02 at 180iterations finished qdiffx linear iterations at : 19:44:35 total time elapsed so far: 11.05000 # loops : 180 mean,max change (kT/e) : 6.9569011E-04 1.3378143E-02 energy calculations done at 11.05000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.22000 DelPhi exited at 19:44:35 11.223u 0.176s 0:11.66 97.6% 0+0k 0+0io 0pf+0w