Mon Oct 10 19:33:27 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 Mon Oct 10 2011 at 19:33:27 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 = 2631 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: 0.5562761 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): -40.10700 23.89000 ymin,ymax (A): -27.14800 29.59000 zmin,zma (A): 0.8600000 63.16300 x,y,z range (A): 63.99700 56.73800 62.30300 scale (grids/A): 0.5562761 object centre (A): -8.108500 1.221001 32.01150 number of atom coordinates read : 2631 total number of charged atoms : 2492 net assigned charge : 9.000031 assigned positive charge : 391.1150 centred at (gu) : 90.62377 89.41544 87.49227 assigned negative charge : -382.1160 centred at (gu) : 90.73512 89.34594 87.45600 start vw surface at 0.1500000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 5421 nv = 96 ne = 84 npr = 50878 no. pairs analyzed = 50878 no. exposed pairs = 3665 no. arc points = 27423 no. surface atoms = 1221 nbur = 1410 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 = 1.540000 m= 232 mr = 2482 m= 3 mr = 19 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3900000 number of dielectric boundary points 3155 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2811 ## 380 charges are in solution ## iepsmp to db, and charging done at 0.5800000 number of grid points assigned charge 7048 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.7556074E-10 6.3321881E-10 midg,1,midg; midg,igrid,midg 3.0083930E-10 1.2290260E-09 1,midg,midg; igrid,midg,midg 1.5073289E-09 -1.0932307E-10 gauss-seidel spectral radius is 0.9833193 estimated iterations to convergence 64 setup time was (sec) 0.8600000 now iterating at: 19:33:29 rms-change max change #iterations 7.1529955E-02 12.40568 at 10iterations 4.9323328E-03 0.8802681 at 20iterations 3.4403062E-04 5.2719593E-02 at 30iterations 2.5978747E-05 4.3907166E-03 at 40iterations 2.2685658E-06 3.9672852E-04 at 50iterations finished qdiffx linear iterations at : 19:33:35 total time elapsed so far: 6.920000 # loops : 50 mean,max change (kT/e) : 2.2685658E-06 3.9672852E-04 energy calculations done at 6.920000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.080000 DelPhi exited at 19:33:35 7.085u 0.734s 0:08.34 93.6% 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 19:33:35 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 = 2631 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: 1.668828 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): -40.10700 23.89000 ymin,ymax (A): -27.14800 29.59000 zmin,zma (A): 0.8600000 63.16300 x,y,z range (A): 63.99700 56.73800 62.30300 scale (grids/A): 1.668828 object centre (A): -8.108500 1.221001 32.01150 number of atom coordinates read : 2631 total number of charged atoms : 2492 net assigned charge : 9.000031 assigned positive charge : 391.1150 centred at (gu) : 91.87054 88.24580 82.47641 assigned negative charge : -382.1160 centred at (gu) : 92.20561 88.03756 82.36805 start vw surface at 0.1300000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 58891 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27423 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 18006 mr = 36703 m= 2277 mr = 11986 m= 68 mr = 1233 m= 0 mr = 13 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 238 time to turn everything in is 0.6200000 number of dielectric boundary points 29307 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 301 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.8700000 number of grid points assigned charge 19124 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) : 0.5562761 object centre at (A) : -8.108500 1.221001 32.01150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.0614952E-02 -3.8071999E-03 midg,1,midg; midg,igrid,midg 1.8866675E-02 1.7509529E-02 1,midg,midg; igrid,midg,midg 1.6289620E-02 -5.9292223E-03 gauss-seidel spectral radius is 0.9982409 estimated iterations to convergence 189 setup time was (sec) 1.210000 now iterating at: 19:33:37 rms-change max change #iterations 3.198176 166.8442 at 10iterations 1.339097 61.76194 at 20iterations 0.5640118 22.37792 at 30iterations 0.2377197 8.674129 at 40iterations 9.9975266E-02 3.787060 at 50iterations 4.2062078E-02 1.608023 at 60iterations 1.7774187E-02 0.6171033 at 70iterations 7.4883834E-03 0.2770576 at 80iterations 3.1599803E-03 0.1449623 at 90iterations 1.3355137E-03 5.4106951E-02 at 100iterations 5.6443230E-04 2.0496368E-02 at 110iterations 2.3817578E-04 9.0446472E-03 at 120iterations finished qdiffx linear iterations at : 19:33:55 total time elapsed so far: 19.18000 # loops : 120 mean,max change (kT/e) : 2.3817578E-04 9.0446472E-03 energy calculations done at 19.18000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.33000 DelPhi exited at 19:33:56 19.339u 0.857s 0:20.57 98.1% 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 19:33:56 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 = 2631 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: 2.503242 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): -40.10700 23.89000 ymin,ymax (A): -27.14800 29.59000 zmin,zma (A): 0.8600000 63.16300 x,y,z range (A): 63.99700 56.73800 62.30300 scale (grids/A): 2.503242 object centre (A): -8.108500 1.221001 32.01150 number of atom coordinates read : 2631 total number of charged atoms : 2492 net assigned charge : 9.000031 assigned positive charge : 391.1150 centred at (gu) : 92.80577 87.36859 78.71445 assigned negative charge : -382.1160 centred at (gu) : 93.30839 87.05631 78.55196 start vw surface at 0.1300000 fill in re-entrant regions at 0.4600000 boundary points on vw surface= 136570 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27423 grid for indexing accessible points = 1.400000 m= 59699 mr = 90409 m= 18988 mr = 45766 m= 3681 mr = 14249 m= 322 mr = 2552 m= 3 mr = 168 m= 0 mr = 0 time to grow re-entrant surface = 0.8500000 no. cavity mid-points inaccessible to solvent = 862 time to turn everything in is 1.460000 number of dielectric boundary points 66119 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 23 iepsmp to db, and charging done at 1.720000 number of grid points assigned charge 19911 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) : 1.668828 object centre at (A) : -8.108500 1.221001 32.01150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.6965860 -7.8287661E-02 midg,1,midg; midg,igrid,midg 0.3152299 0.2166755 1,midg,midg; igrid,midg,midg 0.3185839 -0.1128362 gauss-seidel spectral radius is 0.9991484 estimated iterations to convergence 271 setup time was (sec) 2.090000 now iterating at: 19:33:59 rms-change max change #iterations 8.182515 313.0681 at 10iterations 4.583438 109.6786 at 20iterations 2.552725 60.97141 at 30iterations 1.418919 33.67242 at 40iterations 0.7858043 18.09148 at 50iterations 0.4338265 9.982418 at 60iterations 0.2402637 5.173158 at 70iterations 0.1325478 2.855420 at 80iterations 7.3161185E-02 1.707570 at 90iterations 4.0336471E-02 0.8367391 at 100iterations 2.2203626E-02 0.4494543 at 110iterations 1.2227274E-02 0.2614079 at 120iterations 6.7418423E-03 0.1455688 at 130iterations 3.7100294E-03 7.7641726E-02 at 140iterations 2.0440985E-03 4.2908430E-02 at 150iterations 1.1256760E-03 2.3758411E-02 at 160iterations 6.1890448E-04 1.3756752E-02 at 170iterations 3.4095941E-04 7.2746277E-03 at 180iterations finished qdiffx linear iterations at : 19:34:30 total time elapsed so far: 32.48000 # loops : 180 mean,max change (kT/e) : 3.4095941E-04 7.2746277E-03 energy calculations done at 32.48000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 32.64000 DelPhi exited at 19:34:30 32.644u 0.993s 0:34.26 98.1% 0+0k 0+0io 0pf+0w