Sun Oct 9 02:15:05 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 Sun Oct 9 2011 at 02:15:05 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 = 1845 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: 0.2340350 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): -114.2920 -61.72100 ymin,ymax (A): -118.3190 33.79500 zmin,zma (A): -2.307000 51.33500 x,y,z range (A): 52.57100 152.1140 53.64200 scale (grids/A): 0.2340350 object centre (A): -88.00650 -42.26200 24.51400 number of atom coordinates read : 1845 total number of charged atoms : 1723 net assigned charge : 6.500015 assigned positive charge : 270.2042 centred at (gu) : 90.66052 76.61996 89.90437 assigned negative charge : -263.7044 centred at (gu) : 90.61744 76.61597 89.92935 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 505 nv = 96 ne = 84 npr = 32120 no. pairs analyzed = 32120 no. exposed pairs = 3174 no. arc points = 22792 no. surface atoms = 1037 nbur = 808 mkacc time = 6.9999993E-02 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 3.640000 m= 10 mr = 97 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2200000 number of dielectric boundary points 418 no. dielectric boundary points in salt = 1 no. grid points charged and at boundary= 703 ## 320 charges are in solution ## iepsmp to db, and charging done at 0.3200000 number of grid points assigned charge 821 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.6431881E-22 7.0272304E-23 midg,1,midg; midg,igrid,midg 3.7634136E-19 2.0744037E-25 1,midg,midg; igrid,midg,midg 6.7734769E-24 4.5036304E-22 gauss-seidel spectral radius is 0.9111066 estimated iterations to convergence 29 setup time was (sec) 0.4500000 now iterating at: 02:15:06 rms-change max change #iterations 4.5611014E-04 0.2510591 at 10iterations 2.5803891E-05 1.3553143E-02 at 20iterations 1.7950001E-06 9.4223022E-04 at 30iterations 1.2513800E-07 6.5803528E-05 at 40iterations 1.0128471E-08 5.7220459E-06 at 50iterations finished qdiffx linear iterations at : 02:15:10 total time elapsed so far: 4.500000 # loops : 50 mean,max change (kT/e) : 1.0128471E-08 5.7220459E-06 energy calculations done at 4.500000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.680000 DelPhi exited at 02:15:10 4.681u 0.179s 0:05.16 93.9% 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 Sun Oct 9 2011 at 02:15:10 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 = 1845 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: 0.7021050 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): -114.2920 -61.72100 ymin,ymax (A): -118.3190 33.79500 zmin,zma (A): -2.307000 51.33500 x,y,z range (A): 52.57100 152.1140 53.64200 scale (grids/A): 0.7021050 object centre (A): -88.00650 -42.26200 24.51400 number of atom coordinates read : 1845 total number of charged atoms : 1723 net assigned charge : 6.500015 assigned positive charge : 270.2042 centred at (gu) : 91.98164 49.86007 89.71323 assigned negative charge : -263.7044 centred at (gu) : 91.85252 49.84819 89.78813 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6697 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22792 initial cube size too small, in assigning accessible points to a grid therefore rescaling... initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 3.377920 m= 466 mr = 2873 m= 5 mr = 37 m= 0 mr = 0 time to grow re-entrant surface = 4.0000007E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2000000 number of dielectric boundary points 4258 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1878 ## 166 charges are in solution ## iepsmp to db, and charging done at 0.3100000 number of grid points assigned charge 6981 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) : 0.2340350 object centre at (A) : -88.00650 -42.26200 24.51400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.2314557E-08 8.4588763E-08 midg,1,midg; midg,igrid,midg 4.5135955E-04 1.9646000E-10 1,midg,midg; igrid,midg,midg -5.7907851E-08 7.6815482E-08 gauss-seidel spectral radius is 0.9893427 estimated iterations to convergence 79 setup time was (sec) 0.4800000 now iterating at: 02:15:11 rms-change max change #iterations 0.1756117 30.07826 at 10iterations 2.0386701E-02 3.012809 at 20iterations 2.4700386E-03 0.3853350 at 30iterations 3.1974219E-04 5.0305128E-02 at 40iterations 5.7090125E-05 7.6971054E-03 at 50iterations 1.5129624E-05 1.7528534E-03 at 60iterations 4.6912915E-06 4.7683716E-04 at 70iterations 1.4968974E-06 1.5258789E-04 at 80iterations 4.8572304E-07 6.1988831E-05 at 90iterations 1.7826390E-07 3.0517578E-05 at 100iterations 1.0467956E-07 3.0517578E-05 at 110iterations 9.5298617E-08 3.0517578E-05 at 120iterations finished qdiffx linear iterations at : 02:15:17 total time elapsed so far: 6.620000 # loops : 120 mean,max change (kT/e) : 9.5298617E-08 3.0517578E-05 energy calculations done at 6.620000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.800000 DelPhi exited at 02:15:17 6.802u 0.191s 0:07.29 95.8% 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 Sun Oct 9 2011 at 02:15:18 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 = 1845 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: 1.053158 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): -114.2920 -61.72100 ymin,ymax (A): -118.3190 33.79500 zmin,zma (A): -2.307000 51.33500 x,y,z range (A): 52.57100 152.1140 53.64200 scale (grids/A): 1.053158 object centre (A): -88.00650 -42.26200 24.51400 number of atom coordinates read : 1845 total number of charged atoms : 1723 net assigned charge : 6.500015 assigned positive charge : 270.2042 centred at (gu) : 92.97250 29.79018 89.56985 assigned negative charge : -263.7044 centred at (gu) : 92.77880 29.77239 89.68221 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 16076 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22792 initial cube size too small, in assigning accessible points to a grid therefore rescaling... initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 3.348800 m= 2278 mr = 7960 m= 62 mr = 762 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2600000 number of dielectric boundary points 9694 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 645 ## 51 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 10597 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) : 0.7021050 object centre at (A) : -88.00650 -42.26200 24.51400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.2187937E-06 1.4072129E-05 midg,1,midg; midg,igrid,midg 9.9388823E-02 4.0465309E-08 1,midg,midg; igrid,midg,midg -7.2708222E-06 9.4759816E-06 gauss-seidel spectral radius is 0.9950936 estimated iterations to convergence 115 setup time was (sec) 0.5300000 now iterating at: 02:15:18 rms-change max change #iterations 0.8929790 120.3499 at 10iterations 0.2157431 25.40097 at 20iterations 5.2338775E-02 5.015361 at 30iterations 1.2571664E-02 1.319032 at 40iterations 2.9895580E-03 0.3066978 at 50iterations 7.1583613E-04 6.5309525E-02 at 60iterations 1.7268250E-04 1.4027596E-02 at 70iterations 4.4123408E-05 3.3187866E-03 at 80iterations 1.2796891E-05 9.2506409E-04 at 90iterations 4.5892507E-06 3.3569336E-04 at 100iterations 1.9589891E-06 1.2207031E-04 at 110iterations 9.1846942E-07 6.1035156E-05 at 120iterations 4.7484204E-07 4.5776367E-05 at 130iterations 3.0614132E-07 3.0517578E-05 at 140iterations 2.5521391E-07 6.1035156E-05 at 150iterations 2.4190160E-07 3.8146973E-05 at 160iterations 2.3654762E-07 6.1035156E-05 at 170iterations 2.3006707E-07 3.0517578E-05 at 180iterations finished qdiffx linear iterations at : 02:15:28 total time elapsed so far: 9.830000 # loops : 180 mean,max change (kT/e) : 2.3006707E-07 3.0517578E-05 energy calculations done at 9.830000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.00000 DelPhi exited at 02:15:28 10.003u 0.228s 0:10.50 97.3% 0+0k 0+0io 0pf+0w