Tue Oct 11 08:23:38 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 Tue Oct 11 2011 at 08:23:39 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: 250 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2142 !!! WARNING: ASP 696 has a net charge of -2.0000 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: 0.7100119 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): 37.21700 82.10900 ymin,ymax (A): 28.82400 78.20800 zmin,zma (A): 1.328000 51.46800 x,y,z range (A): 44.89200 49.38400 50.14000 scale (grids/A): 0.7100119 object centre (A): 59.66300 53.51600 26.39800 number of atom coordinates read : 2142 total number of charged atoms : 2022 net assigned charge : 1.000010 assigned positive charge : 318.2015 centred at (gu) : 89.38294 89.80982 89.76665 assigned negative charge : -317.2019 centred at (gu) : 89.32809 89.81654 89.53757 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7342 nv = 96 ne = 84 npr = 44355 no. pairs analyzed = 44355 no. exposed pairs = 2739 no. arc points = 19353 no. surface atoms = 919 nbur = 1223 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 453 mr = 3975 m= 2 mr = 61 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 7 time to turn everything in is 0.2900000 number of dielectric boundary points 3761 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1699 ## 125 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 8158 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.2062131E-07 1.2300980E-07 midg,1,midg; midg,igrid,midg 1.3699400E-08 5.8595386E-09 1,midg,midg; igrid,midg,midg -2.2375044E-08 3.4274503E-08 gauss-seidel spectral radius is 0.9896724 estimated iterations to convergence 80 setup time was (sec) 0.5100000 now iterating at: 08:23:39 rms-change max change #iterations 0.2064994 30.83012 at 10iterations 2.5603088E-02 3.413847 at 20iterations 3.1633200E-03 0.4539080 at 30iterations 4.1938847E-04 5.4405212E-02 at 40iterations 6.8339075E-05 1.1575699E-02 at 50iterations finished qdiffx linear iterations at : 08:23:42 total time elapsed so far: 3.190000 # loops : 50 mean,max change (kT/e) : 6.8339075E-05 1.1575699E-02 energy calculations done at 3.190000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.400000 DelPhi exited at 08:23:42 3.406u 0.165s 0:03.92 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 08:23:42 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: 250 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2142 !!! WARNING: ASP 696 has a net charge of -2.0000 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: 2.130036 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): 37.21700 82.10900 ymin,ymax (A): 28.82400 78.20800 zmin,zma (A): 1.328000 51.46800 x,y,z range (A): 44.89200 49.38400 50.14000 scale (grids/A): 2.130036 object centre (A): 59.66300 53.51600 26.39800 number of atom coordinates read : 2142 total number of charged atoms : 2022 net assigned charge : 1.000010 assigned positive charge : 318.2015 centred at (gu) : 88.14833 89.42924 89.29951 assigned negative charge : -317.2019 centred at (gu) : 87.98424 89.44955 88.61283 start vw surface at 0.1500000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 78142 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19353 grid for indexing accessible points = 1.400000 m= 29548 mr = 53748 m= 5994 mr = 21824 m= 562 mr = 3805 m= 20 mr = 221 m= 1 mr = 1 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 203 time to turn everything in is 0.6000000 number of dielectric boundary points 34668 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 67 iepsmp to db, and charging done at 0.7200000 number of grid points assigned charge 16066 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) : 0.7100119 object centre at (A) : 59.66300 53.51600 26.39800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.2745441E-02 7.2081037E-02 midg,1,midg; midg,igrid,midg -3.8977131E-02 -3.3392664E-02 1,midg,midg; igrid,midg,midg -1.1236377E-02 5.0197048E-03 gauss-seidel spectral radius is 0.9988554 estimated iterations to convergence 234 setup time was (sec) 0.8900000 now iterating at: 08:23:43 rms-change max change #iterations 4.728135 208.1921 at 10iterations 2.349941 76.87231 at 20iterations 1.177076 35.80678 at 30iterations 0.5870390 18.32256 at 40iterations 0.2937827 8.255519 at 50iterations 0.1469940 4.451304 at 60iterations 7.3067687E-02 2.217855 at 70iterations 3.6523819E-02 1.020727 at 80iterations 1.8289838E-02 0.5693436 at 90iterations 9.1380877E-03 0.2662964 at 100iterations 4.5588734E-03 0.1461868 at 110iterations 2.2857888E-03 6.8145752E-02 at 120iterations finished qdiffx linear iterations at : 08:23:50 total time elapsed so far: 7.290000 # loops : 120 mean,max change (kT/e) : 2.2857888E-03 6.8145752E-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) 7.470000 DelPhi exited at 08:23:51 7.474u 0.165s 0:08.26 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 Tue Oct 11 2011 at 08:23:51 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: 250 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2142 !!! WARNING: ASP 696 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.195054 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): 37.21700 82.10900 ymin,ymax (A): 28.82400 78.20800 zmin,zma (A): 1.328000 51.46800 x,y,z range (A): 44.89200 49.38400 50.14000 scale (grids/A): 3.195054 object centre (A): 59.66300 53.51600 26.39800 number of atom coordinates read : 2142 total number of charged atoms : 2022 net assigned charge : 1.000010 assigned positive charge : 318.2015 centred at (gu) : 87.22251 89.14387 88.94929 assigned negative charge : -317.2019 centred at (gu) : 86.97646 89.17420 87.91922 start vw surface at 0.1400000 fill in re-entrant regions at 0.8700000 boundary points on vw surface= 180745 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19353 grid for indexing accessible points = 1.400000 m= 92213 mr = 130636 m= 37851 mr = 75353 m= 11113 mr = 30536 m= 2197 mr = 8267 m= 251 mr = 1492 m= 13 mr = 111 m= 1 mr = 1 m= 0 mr = 0 time to grow re-entrant surface = 0.9100000 no. cavity mid-points inaccessible to solvent = 657 time to turn everything in is 1.920000 number of dielectric boundary points 77988 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.060000 number of grid points assigned charge 16176 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) : 2.130036 object centre at (A) : 59.66300 53.51600 26.39800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.5762745 0.3576463 midg,1,midg; midg,igrid,midg -0.4121175 -0.3020993 1,midg,midg; igrid,midg,midg -0.1201598 4.2836326E-03 gauss-seidel spectral radius is 0.9993150 estimated iterations to convergence 301 setup time was (sec) 2.220000 now iterating at: 08:23:53 rms-change max change #iterations 10.51222 418.4388 at 10iterations 6.227987 120.9930 at 20iterations 3.694346 78.35042 at 30iterations 2.187544 42.61983 at 40iterations 1.287556 24.70072 at 50iterations 0.7614602 14.51483 at 60iterations 0.4484215 8.146641 at 70iterations 0.2630666 4.525814 at 80iterations 0.1549159 2.727747 at 90iterations 9.1027044E-02 1.595247 at 100iterations 5.3508945E-02 0.9042511 at 110iterations 3.1395510E-02 0.5115166 at 120iterations 1.8452516E-02 0.3827248 at 130iterations 1.0836031E-02 0.1748290 at 140iterations 6.3612633E-03 0.1011047 at 150iterations 3.7357544E-03 6.2141418E-02 at 160iterations 2.1965632E-03 3.6838233E-02 at 170iterations 1.2886442E-03 2.2179127E-02 at 180iterations finished qdiffx linear iterations at : 08:24:03 total time elapsed so far: 12.32000 # loops : 180 mean,max change (kT/e) : 1.2886442E-03 2.2179127E-02 energy calculations done at 12.32000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.52000 DelPhi exited at 08:24:04 12.520u 0.175s 0:13.01 97.5% 0+0k 0+0io 0pf+0w