Tue Oct 11 06:09:05 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 Tue Oct 11 2011 at 06:09:05 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 = 2040 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.7195408 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): 3.574000 46.49900 ymin,ymax (A): 0.5849999 40.25900 zmin,zma (A): -2.153000 47.32300 x,y,z range (A): 42.92500 39.67400 49.47600 scale (grids/A): 0.7195408 object centre (A): 25.03650 20.42200 22.58500 number of atom coordinates read : 2040 total number of charged atoms : 1912 net assigned charge : 7.500009 assigned positive charge : 309.1790 centred at (gu) : 90.25524 90.56264 90.21684 assigned negative charge : -301.6792 centred at (gu) : 90.44492 90.52978 90.24921 start vw surface at 0.1400000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 7150 nv = 96 ne = 84 npr = 41067 no. pairs analyzed = 41067 no. exposed pairs = 2478 no. arc points = 16783 no. surface atoms = 846 nbur = 1194 mkacc time = 8.9999989E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 484 mr = 4125 m= 3 mr = 94 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2600000 number of dielectric boundary points 3418 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1582 ## 136 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 7814 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0019553E-07 6.6543230E-08 midg,1,midg; midg,igrid,midg 5.7520232E-08 1.1631553E-07 1,midg,midg; igrid,midg,midg 1.9075476E-07 -3.8422009E-08 gauss-seidel spectral radius is 0.9899231 estimated iterations to convergence 81 setup time was (sec) 0.5300000 now iterating at: 06:09:06 rms-change max change #iterations 0.2109884 30.49441 at 10iterations 2.7382851E-02 3.527052 at 20iterations 3.6087523E-03 0.5150862 at 30iterations 5.5970583E-04 7.0175171E-02 at 40iterations 1.3399399E-04 2.0576477E-02 at 50iterations finished qdiffx linear iterations at : 06:09:09 total time elapsed so far: 3.990000 # loops : 50 mean,max change (kT/e) : 1.3399399E-04 2.0576477E-02 energy calculations done at 3.990000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.180000 DelPhi exited at 06:09:10 4.179u 0.214s 0:04.82 90.8% 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 Tue Oct 11 2011 at 06:09:10 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 = 2040 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.158622 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): 3.574000 46.49900 ymin,ymax (A): 0.5849999 40.25900 zmin,zma (A): -2.153000 47.32300 x,y,z range (A): 42.92500 39.67400 49.47600 scale (grids/A): 2.158622 object centre (A): 25.03650 20.42200 22.58500 number of atom coordinates read : 2040 total number of charged atoms : 1912 net assigned charge : 7.500009 assigned positive charge : 309.1790 centred at (gu) : 90.76583 91.68816 90.65061 assigned negative charge : -301.6792 centred at (gu) : 91.33505 91.58938 90.74770 start vw surface at 0.1500000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 76175 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16783 grid for indexing accessible points = 1.400000 m= 30972 mr = 54451 m= 6089 mr = 23763 m= 576 mr = 4113 m= 14 mr = 286 m= 0 mr = 3 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6700000 number of dielectric boundary points 31210 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 59 iepsmp to db, and charging done at 0.8000000 number of grid points assigned charge 15186 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) : 0.7195408 object centre at (A) : 25.03650 20.42200 22.58500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.5925673E-02 6.0623139E-02 midg,1,midg; midg,igrid,midg 5.2083652E-03 3.6410827E-02 1,midg,midg; igrid,midg,midg 4.9289387E-02 1.7357790E-03 gauss-seidel spectral radius is 0.9988589 estimated iterations to convergence 234 setup time was (sec) 1.000000 now iterating at: 06:09:11 rms-change max change #iterations 4.663129 251.8740 at 10iterations 2.328841 96.59039 at 20iterations 1.168484 38.30725 at 30iterations 0.5863269 18.04225 at 40iterations 0.2938360 8.500065 at 50iterations 0.1477711 4.915440 at 60iterations 7.3770195E-02 2.172650 at 70iterations 3.7141740E-02 1.235853 at 80iterations 1.8614860E-02 0.5300140 at 90iterations 9.3962504E-03 0.2817612 at 100iterations 4.7553722E-03 0.1499634 at 110iterations 2.4418742E-03 7.3596954E-02 at 120iterations finished qdiffx linear iterations at : 06:09:20 total time elapsed so far: 9.580000 # loops : 120 mean,max change (kT/e) : 2.4418742E-03 7.3596954E-02 energy calculations done at 9.580000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.750000 DelPhi exited at 06:09:20 9.751u 0.280s 0:10.49 95.6% 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 Tue Oct 11 2011 at 06:09:20 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 = 2040 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: 3.237933 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): 3.574000 46.49900 ymin,ymax (A): 0.5849999 40.25900 zmin,zma (A): -2.153000 47.32300 x,y,z range (A): 42.92500 39.67400 49.47600 scale (grids/A): 3.237933 object centre (A): 25.03650 20.42200 22.58500 number of atom coordinates read : 2040 total number of charged atoms : 1912 net assigned charge : 7.500009 assigned positive charge : 309.1790 centred at (gu) : 91.14870 92.53220 90.97585 assigned negative charge : -301.6792 centred at (gu) : 92.00258 92.38410 91.12157 start vw surface at 0.1500000 fill in re-entrant regions at 0.9100000 boundary points on vw surface= 175501 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16783 grid for indexing accessible points = 1.400000 m= 96302 mr = 130929 m= 39720 mr = 80581 m= 11783 mr = 33007 m= 2438 mr = 9167 m= 267 mr = 1783 m= 7 mr = 185 m= 0 mr = 2 time to grow re-entrant surface = 0.9800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.020000 number of dielectric boundary points 70364 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.180000 number of grid points assigned charge 15296 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) : 2.158622 object centre at (A) : 25.03650 20.42200 22.58500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3873648 0.6504964 midg,1,midg; midg,igrid,midg 1.2246624E-03 0.2604024 1,midg,midg; igrid,midg,midg 0.3537844 9.0988196E-02 gauss-seidel spectral radius is 0.9993005 estimated iterations to convergence 298 setup time was (sec) 2.380000 now iterating at: 06:09:23 rms-change max change #iterations 10.32099 304.3253 at 10iterations 6.119455 157.1529 at 20iterations 3.619888 71.38834 at 30iterations 2.141883 45.48856 at 40iterations 1.263984 26.57196 at 50iterations 0.7449579 14.78167 at 60iterations 0.4384382 7.793384 at 70iterations 0.2574309 5.075587 at 80iterations 0.1514400 2.552370 at 90iterations 8.9176290E-02 1.577706 at 100iterations 5.2333735E-02 1.049429 at 110iterations 3.0785847E-02 0.5745049 at 120iterations 1.8204909E-02 0.3302923 at 130iterations 1.0846505E-02 0.1905947 at 140iterations 6.5544532E-03 0.1309414 at 150iterations 4.0594679E-03 7.1113586E-02 at 160iterations 2.6191834E-03 4.5656681E-02 at 170iterations 1.7817625E-03 3.2535553E-02 at 180iterations finished qdiffx linear iterations at : 06:09:37 total time elapsed so far: 16.06000 # loops : 180 mean,max change (kT/e) : 1.7817625E-03 3.2535553E-02 energy calculations done at 16.06000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.23000 DelPhi exited at 06:09:37 16.236u 0.262s 0:16.83 97.9% 0+0k 0+0io 0pf+0w