Sun Oct 9 15:11:05 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 15:11:05 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 = 5351 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5123703 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): -16.52100 52.96000 ymin,ymax (A): 97.08000 163.5870 zmin,zma (A): -29.95500 31.89400 x,y,z range (A): 69.48100 66.50700 61.84900 scale (grids/A): 0.5123703 object centre (A): 18.21950 130.3335 0.9695005 number of atom coordinates read : 5351 total number of charged atoms : 5180 net assigned charge : -5.499962 assigned positive charge : 815.4696 centred at (gu) : 89.41743 88.98601 88.40104 assigned negative charge : -820.9760 centred at (gu) : 89.45177 89.06957 88.34437 start vw surface at 0.1400000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 8620 nv = 96 ne = 84 npr = 110641 no. pairs analyzed = 110641 no. exposed pairs = 6198 no. arc points = 43114 no. surface atoms = 2073 nbur = 3278 mkacc time = 0.1900000 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 = 1.680000 m= 290 mr = 4733 m= 0 mr = 3 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 46 time to turn everything in is 0.3500000 number of dielectric boundary points 4174 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4186 ## 606 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 11777 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.0873618E-10 6.1617184E-11 midg,1,midg; midg,igrid,midg 2.3764923E-10 -2.7198385E-10 1,midg,midg; igrid,midg,midg 2.9800044E-11 -1.6738273E-10 gauss-seidel spectral radius is 0.9805478 estimated iterations to convergence 59 setup time was (sec) 0.5400000 now iterating at: 15:11:06 rms-change max change #iterations 7.2351374E-02 12.74959 at 10iterations 4.4443384E-03 0.5791073 at 20iterations 4.4102751E-04 6.1364174E-02 at 30iterations 8.6845146E-05 1.1755466E-02 at 40iterations 1.9779238E-05 2.6350021E-03 at 50iterations finished qdiffx linear iterations at : 15:11:09 total time elapsed so far: 3.480000 # loops : 50 mean,max change (kT/e) : 1.9779238E-05 2.6350021E-03 energy calculations done at 3.480000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.620000 DelPhi exited at 15:11:10 3.620u 0.192s 0:04.14 92.0% 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 15:11:10 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 = 5351 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.537111 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): -16.52100 52.96000 ymin,ymax (A): 97.08000 163.5870 zmin,zma (A): -29.95500 31.89400 x,y,z range (A): 69.48100 66.50700 61.84900 scale (grids/A): 1.537111 object centre (A): 18.21950 130.3335 0.9695005 number of atom coordinates read : 5351 total number of charged atoms : 5180 net assigned charge : -5.499962 assigned positive charge : 815.4696 centred at (gu) : 88.25072 86.95654 85.20155 assigned negative charge : -820.9760 centred at (gu) : 88.35520 87.20842 85.03316 start vw surface at 0.1400000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 98777 reading accessible surface arcs data from file ARCDAT no. of arc points read = 43114 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 28412 mr = 70123 m= 2424 mr = 19469 m= 46 mr = 1128 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 3641 time to turn everything in is 0.4800000 number of dielectric boundary points 38940 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 517 ## 6 charges are in solution ## iepsmp to db, and charging done at 0.5500000 number of grid points assigned charge 38908 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) : 0.5123703 object centre at (A) : 18.21950 130.3335 0.9695005 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.1680696E-03 -5.5776592E-03 midg,1,midg; midg,igrid,midg 1.4281195E-02 -1.6690688E-02 1,midg,midg; igrid,midg,midg -2.7170738E-02 -4.5620473E-03 gauss-seidel spectral radius is 0.9981610 estimated iterations to convergence 185 setup time was (sec) 0.6900000 now iterating at: 15:11:11 rms-change max change #iterations 4.102898 151.8363 at 10iterations 1.697743 54.14115 at 20iterations 0.7059966 22.86309 at 30iterations 0.2935577 8.921438 at 40iterations 0.1220395 4.179741 at 50iterations 5.0623909E-02 1.557640 at 60iterations 2.1139126E-02 0.6252213 at 70iterations 8.8192010E-03 0.2615948 at 80iterations 3.6584991E-03 0.1141586 at 90iterations 1.5345181E-03 4.5051575E-02 at 100iterations 6.4178579E-04 1.9218445E-02 at 110iterations 2.7101539E-04 8.4123611E-03 at 120iterations finished qdiffx linear iterations at : 15:11:18 total time elapsed so far: 7.970000 # loops : 120 mean,max change (kT/e) : 2.7101539E-04 8.4123611E-03 energy calculations done at 7.970000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.120000 DelPhi exited at 15:11:18 8.119u 0.225s 0:08.62 96.6% 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 Sun Oct 9 2011 at 15:11:18 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 = 5351 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: 2.305666 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): -16.52100 52.96000 ymin,ymax (A): 97.08000 163.5870 zmin,zma (A): -29.95500 31.89400 x,y,z range (A): 69.48100 66.50700 61.84900 scale (grids/A): 2.305666 object centre (A): 18.21950 130.3335 0.9695005 number of atom coordinates read : 5351 total number of charged atoms : 5180 net assigned charge : -5.499962 assigned positive charge : 815.4696 centred at (gu) : 87.37566 85.43437 82.80177 assigned negative charge : -820.9760 centred at (gu) : 87.53267 85.81264 82.54960 start vw surface at 0.1400000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 230903 reading accessible surface arcs data from file ARCDAT no. of arc points read = 43114 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 102621 mr = 172091 m= 25785 mr = 81661 m= 3629 mr = 19212 m= 202 mr = 2296 m= 1 mr = 61 m= 0 mr = 0 time to grow re-entrant surface = 0.6400000 no. cavity mid-points inaccessible to solvent = 12465 time to turn everything in is 1.150000 number of dielectric boundary points 87820 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 72 iepsmp to db, and charging done at 1.240000 number of grid points assigned charge 41327 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) : 1.537111 object centre at (A) : 18.21950 130.3335 0.9695005 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.6704857E-03 -0.1458387 midg,1,midg; midg,igrid,midg 0.2571518 -0.3717065 1,midg,midg; igrid,midg,midg -0.3582626 6.1124768E-03 gauss-seidel spectral radius is 0.9991776 estimated iterations to convergence 275 setup time was (sec) 1.390000 now iterating at: 15:11:20 rms-change max change #iterations 10.96074 289.0742 at 10iterations 6.249169 128.8078 at 20iterations 3.534539 77.98044 at 30iterations 1.995027 39.04685 at 40iterations 1.121268 20.39401 at 50iterations 0.6285866 11.61499 at 60iterations 0.3528124 6.327942 at 70iterations 0.1975957 3.389434 at 80iterations 0.1103397 1.840118 at 90iterations 6.1734594E-02 1.045227 at 100iterations 3.4484930E-02 0.6247711 at 110iterations 1.9254871E-02 0.3402805 at 120iterations 1.0755184E-02 0.1924686 at 130iterations 6.0018557E-03 0.1015959 at 140iterations 3.3461789E-03 6.1614990E-02 at 150iterations 1.8700052E-03 3.1614304E-02 at 160iterations 1.0460374E-03 1.8997192E-02 at 170iterations 5.8571453E-04 1.0857105E-02 at 180iterations finished qdiffx linear iterations at : 15:11:32 total time elapsed so far: 13.08000 # loops : 180 mean,max change (kT/e) : 5.8571453E-04 1.0857105E-02 energy calculations done at 13.08000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.21000 DelPhi exited at 15:11:32 13.210u 0.226s 0:13.77 97.5% 0+0k 0+0io 0pf+0w