Sun Oct 9 03:29:44 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 Sun Oct 9 2011 at 03:29:44 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: 378 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4238 !!! WARNING: HIR 90 has a net charge of 0.5140 !!! WARNING: GLM 192 has a net charge of -0.0940 !!! WARNING: HIZ 388 has a net charge of 0.2000 !!! WARNING: HEM 601 has a net charge of 1.4000 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: 0.5408115 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): -3.499000 54.18600 ymin,ymax (A): 17.77000 83.59700 zmin,zma (A): -18.22600 44.93500 x,y,z range (A): 57.68500 65.82700 63.16100 scale (grids/A): 0.5408115 object centre (A): 25.34350 50.68350 13.35450 number of atom coordinates read : 4238 total number of charged atoms : 4043 net assigned charge : 12.02002 assigned positive charge : 625.7187 centred at (gu) : 90.20687 92.12489 90.14098 assigned negative charge : -613.7031 centred at (gu) : 90.24011 92.11554 90.12543 start vw surface at 0.1100000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 7907 nv = 96 ne = 84 npr = 86701 no. pairs analyzed = 86701 no. exposed pairs = 5263 no. arc points = 36915 no. surface atoms = 1799 nbur = 2439 mkacc time = 0.1400000 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 = 1.568000 m= 350 mr = 4125 m= 0 mr = 17 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2800000 number of dielectric boundary points 4115 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3619 ## 443 charges are in solution ## iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 10469 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.7233278E-10 7.4726930E-10 midg,1,midg; midg,igrid,midg 3.2290984E-10 1.1409187E-09 1,midg,midg; igrid,midg,midg 8.1171081E-10 3.7249059E-10 gauss-seidel spectral radius is 0.9824733 estimated iterations to convergence 62 setup time was (sec) 0.5000000 now iterating at: 03:29:45 rms-change max change #iterations 8.5190885E-02 12.21666 at 10iterations 7.3739933E-03 1.112261 at 20iterations 1.4385082E-03 0.1841011 at 30iterations 4.2905324E-04 5.2890778E-02 at 40iterations 1.3203766E-04 1.5832901E-02 at 50iterations finished qdiffx linear iterations at : 03:29:48 total time elapsed so far: 3.530000 # loops : 50 mean,max change (kT/e) : 1.3203766E-04 1.5832901E-02 energy calculations done at 3.530000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.660000 DelPhi exited at 03:29:48 3.665u 0.196s 0:04.17 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 Sun Oct 9 2011 at 03:29:48 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: 378 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4238 !!! WARNING: HIR 90 has a net charge of 0.5140 !!! WARNING: GLM 192 has a net charge of -0.0940 !!! WARNING: HIZ 388 has a net charge of 0.2000 !!! WARNING: HEM 601 has a net charge of 1.4000 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: 1.622435 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): -3.499000 54.18600 ymin,ymax (A): 17.77000 83.59700 zmin,zma (A): -18.22600 44.93500 x,y,z range (A): 57.68500 65.82700 63.16100 scale (grids/A): 1.622435 object centre (A): 25.34350 50.68350 13.35450 number of atom coordinates read : 4238 total number of charged atoms : 4043 net assigned charge : 12.02002 assigned positive charge : 625.7187 centred at (gu) : 90.61932 96.37296 90.42158 assigned negative charge : -613.7031 centred at (gu) : 90.72015 96.34644 90.37634 start vw surface at 0.1100000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 88071 reading accessible surface arcs data from file ARCDAT no. of arc points read = 36915 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 27571 mr = 59994 m= 2928 mr = 19017 m= 83 mr = 1450 m= 0 mr = 5 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 946 time to turn everything in is 0.4400000 number of dielectric boundary points 38187 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 389 ## 5 charges are in solution ## iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 30928 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) : 0.5408115 object centre at (A) : 25.34350 50.68350 13.35450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.9044783E-02 7.0244856E-03 midg,1,midg; midg,igrid,midg 1.3573840E-02 2.3627087E-02 1,midg,midg; igrid,midg,midg 3.9451565E-03 -2.5799987E-03 gauss-seidel spectral radius is 0.9982976 estimated iterations to convergence 192 setup time was (sec) 0.6700000 now iterating at: 03:29:49 rms-change max change #iterations 4.009020 166.4256 at 10iterations 1.714253 63.66998 at 20iterations 0.7360190 23.07839 at 30iterations 0.3149199 11.00806 at 40iterations 0.1355620 5.337436 at 50iterations 5.8408353E-02 1.781380 at 60iterations 2.5338251E-02 0.8354416 at 70iterations 1.1037710E-02 0.3625946 at 80iterations 4.9417792E-03 0.1537209 at 90iterations 2.3136437E-03 7.3133469E-02 at 100iterations 1.1396378E-03 3.7683487E-02 at 110iterations 6.1528391E-04 1.8480301E-02 at 120iterations finished qdiffx linear iterations at : 03:29:57 total time elapsed so far: 8.260000 # loops : 120 mean,max change (kT/e) : 6.1528391E-04 1.8480301E-02 energy calculations done at 8.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.390000 DelPhi exited at 03:29:57 8.390u 0.246s 0:08.92 96.7% 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 Sun Oct 9 2011 at 03:29:57 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: 378 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4238 !!! WARNING: HIR 90 has a net charge of 0.5140 !!! WARNING: GLM 192 has a net charge of -0.0940 !!! WARNING: HIZ 388 has a net charge of 0.2000 !!! WARNING: HEM 601 has a net charge of 1.4000 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: 2.433652 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): -3.499000 54.18600 ymin,ymax (A): 17.77000 83.59700 zmin,zma (A): -18.22600 44.93500 x,y,z range (A): 57.68500 65.82700 63.16100 scale (grids/A): 2.433652 object centre (A): 25.34350 50.68350 13.35450 number of atom coordinates read : 4238 total number of charged atoms : 4043 net assigned charge : 12.02002 assigned positive charge : 625.7187 centred at (gu) : 90.92870 99.55895 90.63195 assigned negative charge : -613.7031 centred at (gu) : 91.08025 99.51973 90.56425 start vw surface at 0.1100000 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 204891 reading accessible surface arcs data from file ARCDAT no. of arc points read = 36915 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 94561 mr = 147201 m= 27695 mr = 74622 m= 4486 mr = 20895 m= 281 mr = 2958 m= 2 mr = 108 m= 0 mr = 0 time to grow re-entrant surface = 0.6000000 no. cavity mid-points inaccessible to solvent = 3117 time to turn everything in is 1.070000 number of dielectric boundary points 86132 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 25 iepsmp to db, and charging done at 1.180000 number of grid points assigned charge 32315 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) : 1.622435 object centre at (A) : 25.34350 50.68350 13.35450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1845634 1.7189622E-02 midg,1,midg; midg,igrid,midg 0.1771042 0.2228608 1,midg,midg; igrid,midg,midg 9.8059531E-03 6.0783707E-02 gauss-seidel spectral radius is 0.9992049 estimated iterations to convergence 280 setup time was (sec) 1.330000 now iterating at: 03:29:59 rms-change max change #iterations 10.38775 340.7777 at 10iterations 6.022933 130.3415 at 20iterations 3.467117 80.28072 at 30iterations 1.989196 38.96503 at 40iterations 1.136375 20.60036 at 50iterations 0.6446785 12.64140 at 60iterations 0.3668776 6.955013 at 70iterations 0.2078201 4.057980 at 80iterations 0.1174010 2.072144 at 90iterations 6.6565886E-02 1.135839 at 100iterations 3.7671119E-02 0.6879616 at 110iterations 2.1313110E-02 0.3681946 at 120iterations 1.2099909E-02 0.2205353 at 130iterations 6.8702335E-03 0.1273193 at 140iterations 3.9332411E-03 7.2814941E-02 at 150iterations 2.2787410E-03 4.1028261E-02 at 160iterations 1.3378190E-03 2.4074554E-02 at 170iterations 8.0922083E-04 1.6071320E-02 at 180iterations finished qdiffx linear iterations at : 03:30:11 total time elapsed so far: 13.63000 # loops : 180 mean,max change (kT/e) : 8.0922083E-04 1.6071320E-02 energy calculations done at 13.63000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.76000 DelPhi exited at 03:30:12 13.763u 0.255s 0:14.30 97.9% 0+0k 0+0io 0pf+0w