Tue Oct 11 03:46:43 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 03:46:43 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 = 2770 !!! WARNING: ILE 14 has a net charge of 0.5000 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: 0.6594180 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): -11.83100 36.71700 ymin,ymax (A): -26.89900 21.94600 zmin,zma (A): -8.264000 45.72300 x,y,z range (A): 48.54800 48.84500 53.98700 scale (grids/A): 0.6594180 object centre (A): 12.44300 -2.476501 18.72950 number of atom coordinates read : 2770 total number of charged atoms : 2622 net assigned charge : 4.000024 assigned positive charge : 421.2176 centred at (gu) : 90.15807 90.58438 91.50106 assigned negative charge : -417.2182 centred at (gu) : 89.95960 90.50755 91.51842 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 7898 nv = 96 ne = 84 npr = 56770 no. pairs analyzed = 56770 no. exposed pairs = 3312 no. arc points = 22706 no. surface atoms = 1108 nbur = 1662 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 449 mr = 4498 m= 5 mr = 81 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 3773 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2202 ## 202 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 9437 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.9992485E-09 8.4243705E-09 midg,1,midg; midg,igrid,midg -5.4837224E-09 2.9204662E-08 1,midg,midg; igrid,midg,midg -3.1369890E-08 5.2256592E-08 gauss-seidel spectral radius is 0.9880890 estimated iterations to convergence 75 setup time was (sec) 0.5900000 now iterating at: 03:46:44 rms-change max change #iterations 0.1712831 22.63794 at 10iterations 1.8416863E-02 2.417639 at 20iterations 1.9855686E-03 0.2875175 at 30iterations 2.2797880E-04 2.7877808E-02 at 40iterations 3.5322359E-05 5.8937073E-03 at 50iterations finished qdiffx linear iterations at : 03:46:48 total time elapsed so far: 4.390000 # loops : 50 mean,max change (kT/e) : 3.5322359E-05 5.8937073E-03 energy calculations done at 4.390000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.560000 DelPhi exited at 03:46:49 4.567u 0.376s 0:05.62 87.7% 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 Tue Oct 11 2011 at 03:46:49 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 = 2770 !!! WARNING: ILE 14 has a net charge of 0.5000 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: 1.978254 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): -11.83100 36.71700 ymin,ymax (A): -26.89900 21.94600 zmin,zma (A): -8.264000 45.72300 x,y,z range (A): 48.54800 48.84500 53.98700 scale (grids/A): 1.978254 object centre (A): 12.44300 -2.476501 18.72950 number of atom coordinates read : 2770 total number of charged atoms : 2622 net assigned charge : 4.000024 assigned positive charge : 421.2176 centred at (gu) : 90.47354 91.75245 94.50270 assigned negative charge : -417.2182 centred at (gu) : 89.87848 91.52217 94.55500 start vw surface at 0.1300000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 84402 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22706 grid for indexing accessible points = 1.400000 m= 32358 mr = 59601 m= 5745 mr = 24529 m= 440 mr = 3907 m= 14 mr = 209 m= 0 mr = 0 time to grow re-entrant surface = 0.3700000 no. cavity mid-points inaccessible to solvent = 190 time to turn everything in is 0.7000000 number of dielectric boundary points 34713 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 138 iepsmp to db, and charging done at 0.8100000 number of grid points assigned charge 20693 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) : 0.6594180 object centre at (A) : 12.44300 -2.476501 18.72950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.6142804E-02 1.2281664E-02 midg,1,midg; midg,igrid,midg -1.3072828E-02 -1.5734259E-02 1,midg,midg; igrid,midg,midg -4.7626914E-03 6.9915764E-02 gauss-seidel spectral radius is 0.9987422 estimated iterations to convergence 223 setup time was (sec) 0.9900000 now iterating at: 03:46:50 rms-change max change #iterations 4.747429 222.7990 at 10iterations 2.292930 73.64958 at 20iterations 1.108867 34.66727 at 30iterations 0.5347618 16.12347 at 40iterations 0.2588603 7.746859 at 50iterations 0.1253584 4.196075 at 60iterations 6.0500517E-02 1.706856 at 70iterations 2.9290495E-02 0.8266401 at 80iterations 1.4150172E-02 0.4020004 at 90iterations 6.8417336E-03 0.1853867 at 100iterations 3.3030035E-03 9.9083662E-02 at 110iterations 1.5993961E-03 4.9072266E-02 at 120iterations finished qdiffx linear iterations at : 03:47:00 total time elapsed so far: 10.55000 # loops : 120 mean,max change (kT/e) : 1.5993961E-03 4.9072266E-02 energy calculations done at 10.55000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.72000 DelPhi exited at 03:47:00 10.727u 0.445s 0:11.45 97.4% 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 03:47:00 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 = 2770 !!! WARNING: ILE 14 has a net charge of 0.5000 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: 2.967381 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): -11.83100 36.71700 ymin,ymax (A): -26.89900 21.94600 zmin,zma (A): -8.264000 45.72300 x,y,z range (A): 48.54800 48.84500 53.98700 scale (grids/A): 2.967381 object centre (A): 12.44300 -2.476501 18.72950 number of atom coordinates read : 2770 total number of charged atoms : 2622 net assigned charge : 4.000024 assigned positive charge : 421.2176 centred at (gu) : 90.71008 92.62839 96.75374 assigned negative charge : -417.2182 centred at (gu) : 89.81763 92.28313 96.83237 start vw surface at 0.1300000 fill in re-entrant regions at 0.6100000 boundary points on vw surface= 194612 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22706 grid for indexing accessible points = 1.400000 m= 102404 mr = 143561 m= 39872 mr = 84809 m= 10752 mr = 33027 m= 1927 mr = 8474 m= 188 mr = 1427 m= 9 mr = 122 m= 1 mr = 1 m= 0 mr = 0 time to grow re-entrant surface = 1.120000 no. cavity mid-points inaccessible to solvent = 601 time to turn everything in is 1.870000 number of dielectric boundary points 78344 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.020000 number of grid points assigned charge 20967 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) : 1.978254 object centre at (A) : 12.44300 -2.476501 18.72950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2147117 0.3362255 midg,1,midg; midg,igrid,midg -0.1506108 -0.2634729 1,midg,midg; igrid,midg,midg -3.4733843E-02 0.5803937 gauss-seidel spectral radius is 0.9992836 estimated iterations to convergence 295 setup time was (sec) 2.220000 now iterating at: 03:47:03 rms-change max change #iterations 10.87971 415.1671 at 10iterations 6.383751 145.8376 at 20iterations 3.750921 75.80917 at 30iterations 2.195804 39.66772 at 40iterations 1.285057 24.87004 at 50iterations 0.7514620 15.51946 at 60iterations 0.4379410 8.384499 at 70iterations 0.2557311 5.660892 at 80iterations 0.1484225 2.752159 at 90iterations 8.6474538E-02 1.502453 at 100iterations 5.0361611E-02 0.8241863 at 110iterations 2.9249646E-02 0.4774284 at 120iterations 1.7025180E-02 0.2791595 at 130iterations 9.8677399E-03 0.1772194 at 140iterations 5.7593947E-03 9.5610619E-02 at 150iterations 3.3500011E-03 5.6076050E-02 at 160iterations 1.9596729E-03 3.2148361E-02 at 170iterations 1.1535103E-03 1.9687653E-02 at 180iterations finished qdiffx linear iterations at : 03:47:20 total time elapsed so far: 18.89000 # loops : 180 mean,max change (kT/e) : 1.1535103E-03 1.9687653E-02 energy calculations done at 18.89000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.05000 DelPhi exited at 03:47:20 19.058u 0.466s 0:20.12 96.9% 0+0k 0+0io 0pf+0w