Mon Oct 10 17:04:10 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 Mon Oct 10 2011 at 17:04:10 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: 299 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2818 !!! WARNING: HIT 107 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: 0.6056997 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): 13.24300 72.01800 ymin,ymax (A): 3.629000 50.11200 zmin,zma (A): 7.469000 63.12600 x,y,z range (A): 58.77500 46.48300 55.65700 scale (grids/A): 0.6056997 object centre (A): 42.63050 26.87050 35.29750 number of atom coordinates read : 2818 total number of charged atoms : 2677 net assigned charge : -0.9859680 assigned positive charge : 428.4502 centred at (gu) : 88.60458 90.25649 90.91203 assigned negative charge : -429.4373 centred at (gu) : 88.51272 90.34690 90.94734 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 6834 nv = 96 ne = 84 npr = 56243 no. pairs analyzed = 56243 no. exposed pairs = 3779 no. arc points = 26780 no. surface atoms = 1270 nbur = 1548 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 345 mr = 3452 m= 0 mr = 34 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3500000 number of dielectric boundary points 3693 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2722 ## 299 charges are in solution ## iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 8569 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0377897E-09 -2.5886082E-09 midg,1,midg; midg,igrid,midg 3.6632268E-09 -5.0710303E-09 1,midg,midg; igrid,midg,midg -6.6923560E-09 2.8740168E-09 gauss-seidel spectral radius is 0.9859149 estimated iterations to convergence 69 setup time was (sec) 0.7400000 now iterating at: 17:04:11 rms-change max change #iterations 0.1225346 18.40216 at 10iterations 1.0510758E-02 1.559074 at 20iterations 9.1228331E-04 0.1415765 at 30iterations 8.0941682E-05 1.4827728E-02 at 40iterations 7.7314899E-06 1.3008118E-03 at 50iterations finished qdiffx linear iterations at : 17:04:17 total time elapsed so far: 6.570000 # loops : 50 mean,max change (kT/e) : 7.7314899E-06 1.3008118E-03 energy calculations done at 6.570000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.740000 DelPhi exited at 17:04:18 6.740u 0.603s 0:07.92 92.6% 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 17:04:18 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: 299 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2818 !!! WARNING: HIT 107 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.817099 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): 13.24300 72.01800 ymin,ymax (A): 3.629000 50.11200 zmin,zma (A): 7.469000 63.12600 x,y,z range (A): 58.77500 46.48300 55.65700 scale (grids/A): 1.817099 object centre (A): 42.63050 26.87050 35.29750 number of atom coordinates read : 2818 total number of charged atoms : 2677 net assigned charge : -0.9859680 assigned positive charge : 428.4502 centred at (gu) : 85.81303 90.76881 92.73526 assigned negative charge : -429.4373 centred at (gu) : 85.53806 91.04064 92.84145 start vw surface at 0.1300000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 73923 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26780 grid for indexing accessible points = 1.400000 m= 24456 mr = 48862 m= 3400 mr = 17001 m= 169 mr = 1871 m= 4 mr = 61 m= 0 mr = 0 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6700000 number of dielectric boundary points 34157 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 235 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.8600000 number of grid points assigned charge 20899 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) : 0.6056997 object centre at (A) : 42.63050 26.87050 35.29750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.7933208E-03 6.2661013E-03 midg,1,midg; midg,igrid,midg 1.1166506E-02 -1.2808935E-02 1,midg,midg; igrid,midg,midg -5.0631452E-02 1.6561761E-02 gauss-seidel spectral radius is 0.9985342 estimated iterations to convergence 207 setup time was (sec) 1.150000 now iterating at: 17:04:21 rms-change max change #iterations 4.133316 160.6640 at 10iterations 1.877756 68.91084 at 20iterations 0.8494102 31.82530 at 30iterations 0.3866097 12.24178 at 40iterations 0.1754748 6.079280 at 50iterations 7.9836614E-02 2.654636 at 60iterations 3.6191311E-02 1.203777 at 70iterations 1.6506970E-02 0.5416946 at 80iterations 7.5172433E-03 0.2436676 at 90iterations 3.4089438E-03 0.1173592 at 100iterations 1.5595068E-03 5.2719831E-02 at 110iterations 7.0808840E-04 2.1477699E-02 at 120iterations finished qdiffx linear iterations at : 17:04:36 total time elapsed so far: 16.32000 # loops : 120 mean,max change (kT/e) : 7.0808840E-04 2.1477699E-02 energy calculations done at 16.32000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.49000 DelPhi exited at 17:04:37 16.497u 0.754s 0:19.03 90.5% 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 17:04:37 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: 299 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2818 !!! WARNING: HIT 107 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: 2.725649 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): 13.24300 72.01800 ymin,ymax (A): 3.629000 50.11200 zmin,zma (A): 7.469000 63.12600 x,y,z range (A): 58.77500 46.48300 55.65700 scale (grids/A): 2.725649 object centre (A): 42.63050 26.87050 35.29750 number of atom coordinates read : 2818 total number of charged atoms : 2677 net assigned charge : -0.9859680 assigned positive charge : 428.4502 centred at (gu) : 83.71935 91.15305 94.10258 assigned negative charge : -429.4373 centred at (gu) : 83.30711 91.56087 94.26218 start vw surface at 0.1300000 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 171101 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26780 grid for indexing accessible points = 1.400000 m= 80661 mr = 119265 m= 26854 mr = 63692 m= 5823 mr = 20520 m= 749 mr = 4165 m= 41 mr = 462 m= 1 mr = 12 m= 0 mr = 0 time to grow re-entrant surface = 0.9900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.670000 number of dielectric boundary points 77114 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 10 iepsmp to db, and charging done at 1.900000 number of grid points assigned charge 21414 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) : 1.817099 object centre at (A) : 42.63050 26.87050 35.29750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.7535933E-02 0.1446473 midg,1,midg; midg,igrid,midg 0.1175730 -0.1212165 1,midg,midg; igrid,midg,midg -0.6528305 0.2103094 gauss-seidel spectral radius is 0.9992498 estimated iterations to convergence 288 setup time was (sec) 2.210000 now iterating at: 17:04:40 rms-change max change #iterations 10.12238 298.1612 at 10iterations 5.967332 137.0631 at 20iterations 3.497939 75.07710 at 30iterations 2.026028 48.42255 at 40iterations 1.175111 22.78758 at 50iterations 0.6775961 14.80660 at 60iterations 0.3915116 7.898282 at 70iterations 0.2247434 4.393331 at 80iterations 0.1287382 2.630037 at 90iterations 7.4045695E-02 1.434824 at 100iterations 4.2404190E-02 0.8313980 at 110iterations 2.4350770E-02 0.4866486 at 120iterations 1.3915520E-02 0.2864666 at 130iterations 7.9887537E-03 0.1470852 at 140iterations 4.5717042E-03 9.3870163E-02 at 150iterations 2.6118110E-03 4.7935486E-02 at 160iterations 1.4964940E-03 2.8137207E-02 at 170iterations 8.5656764E-04 1.5528679E-02 at 180iterations finished qdiffx linear iterations at : 17:05:01 total time elapsed so far: 23.21000 # loops : 180 mean,max change (kT/e) : 8.5656764E-04 1.5528679E-02 energy calculations done at 23.21000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 23.37000 DelPhi exited at 17:05:02 23.375u 0.735s 0:24.72 97.4% 0+0k 0+0io 0pf+0w