Mon Oct 10 14:01:49 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 Mon Oct 10 2011 at 14:01:49 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 = 2850 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: 0.5886340 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): -8.882999 46.66300 ymin,ymax (A): -51.93300 8.546000 zmin,zma (A): -32.58800 21.68600 x,y,z range (A): 55.54600 60.47900 54.27400 scale (grids/A): 0.5886340 object centre (A): 18.89000 -21.69350 -5.451001 number of atom coordinates read : 2850 total number of charged atoms : 2778 net assigned charge : 5.500014 assigned positive charge : 424.9379 centred at (gu) : 90.79968 88.77509 90.10030 assigned negative charge : -419.4397 centred at (gu) : 90.73872 88.74899 90.09745 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6882 nv = 96 ne = 84 npr = 53822 no. pairs analyzed = 53822 no. exposed pairs = 4140 no. arc points = 28940 no. surface atoms = 1377 nbur = 1473 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 351 mr = 3285 m= 0 mr = 22 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3100000 number of dielectric boundary points 3926 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2977 ## 306 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 8626 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.4953163E-09 1.7243719E-09 midg,1,midg; midg,igrid,midg 1.1556458E-09 1.7624027E-09 1,midg,midg; igrid,midg,midg -5.3909495E-11 3.9339345E-09 gauss-seidel spectral radius is 0.9851095 estimated iterations to convergence 67 setup time was (sec) 0.5500000 now iterating at: 14:01:50 rms-change max change #iterations 0.1016931 19.68256 at 10iterations 8.1607718E-03 1.325836 at 20iterations 7.3652912E-04 0.1142883 at 30iterations 1.2691047E-04 2.0680904E-02 at 40iterations 3.8406055E-05 6.9804192E-03 at 50iterations finished qdiffx linear iterations at : 14:01:52 total time elapsed so far: 3.260000 # loops : 50 mean,max change (kT/e) : 3.8406055E-05 6.9804192E-03 energy calculations done at 3.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.450000 DelPhi exited at 14:01:53 3.451u 0.192s 0:04.06 89.6% 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 Mon Oct 10 2011 at 14:01:53 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 = 2850 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 1.765902 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): -8.882999 46.66300 ymin,ymax (A): -51.93300 8.546000 zmin,zma (A): -32.58800 21.68600 x,y,z range (A): 55.54600 60.47900 54.27400 scale (grids/A): 1.765902 object centre (A): 18.89000 -21.69350 -5.451001 number of atom coordinates read : 2850 total number of charged atoms : 2778 net assigned charge : 5.500014 assigned positive charge : 424.9379 centred at (gu) : 92.39799 86.32436 90.29966 assigned negative charge : -419.4397 centred at (gu) : 92.21621 86.24692 90.29210 start vw surface at 0.2200000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 74249 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28940 grid for indexing accessible points = 1.400000 m= 25077 mr = 48105 m= 3659 mr = 16844 m= 160 mr = 1970 m= 2 mr = 23 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6000000 number of dielectric boundary points 36205 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 263 iepsmp to db, and charging done at 0.7100000 number of grid points assigned charge 21687 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) : 0.5886340 object centre at (A) : 18.89000 -21.69350 -5.451001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.0578990E-03 -7.1981861E-03 midg,1,midg; midg,igrid,midg 2.6794204E-03 -1.8569188E-02 1,midg,midg; igrid,midg,midg 5.0475979E-03 3.2233566E-02 gauss-seidel spectral radius is 0.9984784 estimated iterations to convergence 203 setup time was (sec) 0.8800000 now iterating at: 14:01:54 rms-change max change #iterations 3.821008 176.2080 at 10iterations 1.708447 60.24271 at 20iterations 0.7631333 26.33710 at 30iterations 0.3430765 10.50775 at 40iterations 0.1540424 5.002593 at 50iterations 6.9034122E-02 2.412524 at 60iterations 3.0882491E-02 1.151165 at 70iterations 1.3825284E-02 0.4589670 at 80iterations 6.2039699E-03 0.1961961 at 90iterations 2.8032782E-03 8.8279724E-02 at 100iterations 1.2602323E-03 4.2846680E-02 at 110iterations 5.7113153E-04 2.3433208E-02 at 120iterations finished qdiffx linear iterations at : 14:02:00 total time elapsed so far: 6.950000 # loops : 120 mean,max change (kT/e) : 5.7113153E-04 2.3433208E-02 energy calculations done at 6.950000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.130000 DelPhi exited at 14:02:02 7.135u 0.203s 0:08.88 82.5% 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 Mon Oct 10 2011 at 14:02:03 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 = 2850 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.648853 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): -8.882999 46.66300 ymin,ymax (A): -51.93300 8.546000 zmin,zma (A): -32.58800 21.68600 x,y,z range (A): 55.54600 60.47900 54.27400 scale (grids/A): 2.648853 object centre (A): 18.89000 -21.69350 -5.451001 number of atom coordinates read : 2850 total number of charged atoms : 2778 net assigned charge : 5.500014 assigned positive charge : 424.9379 centred at (gu) : 93.59673 84.48625 90.44927 assigned negative charge : -419.4397 centred at (gu) : 93.32433 84.37027 90.43810 start vw surface at 0.1500000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 171772 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28940 grid for indexing accessible points = 1.400000 m= 81080 mr = 118487 m= 28397 mr = 62265 m= 6415 mr = 21236 m= 708 mr = 4401 m= 23 mr = 381 m= 0 mr = 0 time to grow re-entrant surface = 0.7800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.330000 number of dielectric boundary points 81625 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 7 iepsmp to db, and charging done at 1.470000 number of grid points assigned charge 22220 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) : 1.765902 object centre at (A) : 18.89000 -21.69350 -5.451001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.4696151E-02 -0.1715754 midg,1,midg; midg,igrid,midg -5.8904342E-02 -0.6520267 1,midg,midg; igrid,midg,midg 5.4717567E-02 0.3513366 gauss-seidel spectral radius is 0.9992384 estimated iterations to convergence 286 setup time was (sec) 1.630000 now iterating at: 14:02:05 rms-change max change #iterations 9.612350 324.6164 at 10iterations 5.696826 152.9953 at 20iterations 3.336854 70.72646 at 30iterations 1.944806 43.20128 at 40iterations 1.128130 25.22326 at 50iterations 0.6523727 13.94203 at 60iterations 0.3753511 8.129039 at 70iterations 0.2155916 4.561541 at 80iterations 0.1238374 2.557144 at 90iterations 7.0993356E-02 1.406252 at 100iterations 4.0678281E-02 0.7905655 at 110iterations 2.3213826E-02 0.4531078 at 120iterations 1.3269724E-02 0.2393730 at 130iterations 7.5977677E-03 0.1461377 at 140iterations 4.3378482E-03 7.9452515E-02 at 150iterations 2.4853572E-03 4.5149326E-02 at 160iterations 1.4209920E-03 2.8435677E-02 at 170iterations 8.1836584E-04 1.5983582E-02 at 180iterations finished qdiffx linear iterations at : 14:02:14 total time elapsed so far: 11.06000 # loops : 180 mean,max change (kT/e) : 8.1836584E-04 1.5983582E-02 energy calculations done at 11.06000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.24000 DelPhi exited at 14:02:15 11.240u 0.188s 0:11.78 96.9% 0+0k 0+0io 0pf+0w