Sun Oct 9 11:17:10 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 11:17:11 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2817 !!! WARNING: HIR 213 has a net charge of 0.5140 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: 0.5808926 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): -22.48700 38.79800 ymin,ymax (A): -25.13600 25.37700 zmin,zma (A): -30.75600 26.13200 x,y,z range (A): 61.28500 50.51300 56.88800 scale (grids/A): 0.5808926 object centre (A): 8.155500 0.1204996 -2.312000 number of atom coordinates read : 2817 total number of charged atoms : 2737 net assigned charge : 5.014011 assigned positive charge : 419.3662 centred at (gu) : 89.32979 90.51828 91.89254 assigned negative charge : -414.3538 centred at (gu) : 89.33952 90.46018 91.85217 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6659 nv = 96 ne = 84 npr = 53748 no. pairs analyzed = 53748 no. exposed pairs = 4043 no. arc points = 28390 no. surface atoms = 1345 nbur = 1472 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 = 1.484000 m= 317 mr = 3320 m= 3 mr = 26 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3400000 number of dielectric boundary points 3633 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2814 ## 260 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 8331 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.7274249E-10 3.0264553E-09 midg,1,midg; midg,igrid,midg -1.1123825E-10 2.6093285E-09 1,midg,midg; igrid,midg,midg 1.5187513E-09 7.6967976E-10 gauss-seidel spectral radius is 0.9847069 estimated iterations to convergence 66 setup time was (sec) 0.5400000 now iterating at: 11:17:11 rms-change max change #iterations 9.6114844E-02 14.90551 at 10iterations 7.4947211E-03 1.037123 at 20iterations 7.2104653E-04 0.1125445 at 30iterations 1.2532991E-04 2.2416115E-02 at 40iterations 3.1287811E-05 5.8002472E-03 at 50iterations finished qdiffx linear iterations at : 11:17:14 total time elapsed so far: 2.970000 # loops : 50 mean,max change (kT/e) : 3.1287811E-05 5.8002472E-03 energy calculations done at 2.970000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.180000 DelPhi exited at 11:17:14 3.179u 0.152s 0:03.72 89.2% 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 11:17:14 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2817 !!! WARNING: HIR 213 has a net charge of 0.5140 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: 1.742678 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): -22.48700 38.79800 ymin,ymax (A): -25.13600 25.37700 zmin,zma (A): -30.75600 26.13200 x,y,z range (A): 61.28500 50.51300 56.88800 scale (grids/A): 1.742678 object centre (A): 8.155500 0.1204996 -2.312000 number of atom coordinates read : 2817 total number of charged atoms : 2737 net assigned charge : 5.014011 assigned positive charge : 419.3662 centred at (gu) : 87.98857 91.55377 95.67690 assigned negative charge : -414.3538 centred at (gu) : 88.01857 91.38035 95.55637 start vw surface at 0.1500000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 72303 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28390 grid for indexing accessible points = 1.400000 m= 23960 mr = 47745 m= 3297 mr = 16182 m= 151 mr = 1811 m= 1 mr = 37 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5300000 number of dielectric boundary points 33937 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 240 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6300000 number of grid points assigned charge 21274 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) : 0.5808926 object centre at (A) : 8.155500 0.1204996 -2.312000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.8066504E-03 1.4274613E-02 midg,1,midg; midg,igrid,midg 9.5028533E-03 1.9885257E-02 1,midg,midg; igrid,midg,midg 1.3053196E-02 -1.3370926E-02 gauss-seidel spectral radius is 0.9984238 estimated iterations to convergence 200 setup time was (sec) 0.8000000 now iterating at: 11:17:15 rms-change max change #iterations 3.701706 179.9946 at 10iterations 1.622588 56.97977 at 20iterations 0.7175241 24.59266 at 30iterations 0.3179838 10.63959 at 40iterations 0.1403334 4.701510 at 50iterations 6.2032066E-02 2.086013 at 60iterations 2.7306901E-02 0.9147878 at 70iterations 1.2168382E-02 0.4242373 at 80iterations 5.4159495E-03 0.1706619 at 90iterations 2.4053385E-03 7.9025269E-02 at 100iterations 1.0823762E-03 3.6102295E-02 at 110iterations 4.9395690E-04 1.6455650E-02 at 120iterations finished qdiffx linear iterations at : 11:17:21 total time elapsed so far: 6.730000 # loops : 120 mean,max change (kT/e) : 4.9395690E-04 1.6455650E-02 energy calculations done at 6.730000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.940000 DelPhi exited at 11:17:22 6.942u 0.179s 0:07.65 92.9% 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 11:17:22 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2817 !!! WARNING: HIR 213 has a net charge of 0.5140 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: 2.614017 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): -22.48700 38.79800 ymin,ymax (A): -25.13600 25.37700 zmin,zma (A): -30.75600 26.13200 x,y,z range (A): 61.28500 50.51300 56.88800 scale (grids/A): 2.614017 object centre (A): 8.155500 0.1204996 -2.312000 number of atom coordinates read : 2817 total number of charged atoms : 2737 net assigned charge : 5.014011 assigned positive charge : 419.3662 centred at (gu) : 86.98262 92.33050 98.51522 assigned negative charge : -414.3538 centred at (gu) : 87.02778 92.07058 98.33459 start vw surface at 0.1400000 fill in re-entrant regions at 0.3900000 boundary points on vw surface= 167478 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28390 grid for indexing accessible points = 1.400000 m= 78680 mr = 116959 m= 26286 mr = 61119 m= 5666 mr = 19792 m= 645 mr = 3931 m= 21 mr = 367 m= 0 mr = 6 time to grow re-entrant surface = 0.7099999 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.200000 number of dielectric boundary points 76602 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 7 iepsmp to db, and charging done at 1.320000 number of grid points assigned charge 21881 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) : 1.742678 object centre at (A) : 8.155500 0.1204996 -2.312000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.4425111E-02 0.1757135 midg,1,midg; midg,igrid,midg 0.1717827 0.2645145 1,midg,midg; igrid,midg,midg 0.2290449 -0.2155407 gauss-seidel spectral radius is 0.9992169 estimated iterations to convergence 282 setup time was (sec) 1.480000 now iterating at: 11:17:24 rms-change max change #iterations 9.318141 314.6759 at 10iterations 5.428102 156.6750 at 20iterations 3.144889 78.91676 at 30iterations 1.805370 40.37080 at 40iterations 1.034088 28.44939 at 50iterations 0.5907094 12.09779 at 60iterations 0.3361578 6.491623 at 70iterations 0.1916466 3.877251 at 80iterations 0.1089377 2.351260 at 90iterations 6.1841402E-02 1.218540 at 100iterations 3.5014253E-02 0.7087536 at 110iterations 1.9842783E-02 0.4280027 at 120iterations 1.1271893E-02 0.2091124 at 130iterations 6.3707903E-03 0.1278448 at 140iterations 3.6167598E-03 7.8880310E-02 at 150iterations 2.0520762E-03 4.1168213E-02 at 160iterations 1.1675877E-03 2.2846222E-02 at 170iterations 6.6722493E-04 1.2853622E-02 at 180iterations finished qdiffx linear iterations at : 11:17:34 total time elapsed so far: 11.46000 # loops : 180 mean,max change (kT/e) : 6.6722493E-04 1.2853622E-02 energy calculations done at 11.46000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.63000 DelPhi exited at 11:17:34 11.634u 0.180s 0:12.32 95.8% 0+0k 0+0io 0pf+0w