Tue Oct 11 06:53:43 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 Tue Oct 11 2011 at 06:53:43 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: 257 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3000 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: 0.6000438 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): -15.30400 44.02500 ymin,ymax (A): 19.34800 76.92400 zmin,zma (A): -69.20700 -20.10600 x,y,z range (A): 59.32900 57.57600 49.10100 scale (grids/A): 0.6000438 object centre (A): 14.36050 48.13600 -44.65650 number of atom coordinates read : 3000 total number of charged atoms : 2839 net assigned charge : -6.499979 assigned positive charge : 434.6584 centred at (gu) : 89.42232 89.90496 89.49631 assigned negative charge : -441.1590 centred at (gu) : 89.38768 90.16829 89.49757 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 6935 nv = 96 ne = 84 npr = 63870 no. pairs analyzed = 63870 no. exposed pairs = 3722 no. arc points = 25843 no. surface atoms = 1263 nbur = 1737 mkacc time = 0.1800000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 359 mr = 3728 m= 1 mr = 39 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 23 time to turn everything in is 0.4000000 number of dielectric boundary points 3528 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2528 ## 241 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 8799 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.0412510E-09 -2.5318549E-09 midg,1,midg; midg,igrid,midg 8.0140055E-09 -1.3750207E-08 1,midg,midg; igrid,midg,midg -4.8030873E-09 -1.1911067E-09 gauss-seidel spectral radius is 0.9856573 estimated iterations to convergence 68 setup time was (sec) 0.6500000 now iterating at: 06:53:44 rms-change max change #iterations 0.1176479 18.67183 at 10iterations 1.0123313E-02 1.642421 at 20iterations 8.7675592E-04 0.1155529 at 30iterations 7.8366968E-05 9.7961426E-03 at 40iterations 7.3924857E-06 1.0859370E-03 at 50iterations finished qdiffx linear iterations at : 06:53:47 total time elapsed so far: 3.970000 # loops : 50 mean,max change (kT/e) : 7.3924857E-06 1.0859370E-03 energy calculations done at 3.970000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.150000 DelPhi exited at 06:53:48 4.154u 0.298s 0:05.09 87.2% 0+0k 0+0io 6pf+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 Tue Oct 11 2011 at 06:53:48 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: 257 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3000 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: 1.800131 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): -15.30400 44.02500 ymin,ymax (A): 19.34800 76.92400 zmin,zma (A): -69.20700 -20.10600 x,y,z range (A): 59.32900 57.57600 49.10100 scale (grids/A): 1.800131 object centre (A): 14.36050 48.13600 -44.65650 number of atom coordinates read : 3000 total number of charged atoms : 2839 net assigned charge : -6.499979 assigned positive charge : 434.6584 centred at (gu) : 88.26647 89.71445 88.48833 assigned negative charge : -441.1590 centred at (gu) : 88.16282 90.50444 88.49226 start vw surface at 0.1700000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 75521 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25843 grid for indexing accessible points = 1.400000 m= 26013 mr = 51738 m= 3776 mr = 18407 m= 159 mr = 2218 m= 0 mr = 36 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6900000 number of dielectric boundary points 33070 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 165 iepsmp to db, and charging done at 0.8200000 number of grid points assigned charge 22213 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) : 0.6000438 object centre at (A) : 14.36050 48.13600 -44.65650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.0677009E-02 1.6287154E-02 midg,1,midg; midg,igrid,midg 3.0176279E-03 -3.5920665E-02 1,midg,midg; igrid,midg,midg -4.0676493E-02 -3.9781269E-02 gauss-seidel spectral radius is 0.9985145 estimated iterations to convergence 206 setup time was (sec) 0.9900000 now iterating at: 06:53:50 rms-change max change #iterations 4.068100 173.5148 at 10iterations 1.820053 61.71442 at 20iterations 0.8289919 29.37755 at 30iterations 0.3744370 13.24971 at 40iterations 0.1702788 5.465508 at 50iterations 7.7218011E-02 2.688679 at 60iterations 3.4990642E-02 1.209034 at 70iterations 1.5854029E-02 0.5031958 at 80iterations 7.1711768E-03 0.2302246 at 90iterations 3.2487253E-03 9.6885681E-02 at 100iterations 1.4783756E-03 4.5749664E-02 at 110iterations 6.6952338E-04 2.2163391E-02 at 120iterations finished qdiffx linear iterations at : 06:53:58 total time elapsed so far: 9.490000 # loops : 120 mean,max change (kT/e) : 6.6952338E-04 2.2163391E-02 energy calculations done at 9.490000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.670000 DelPhi exited at 06:53:59 9.671u 0.312s 0:10.84 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 Tue Oct 11 2011 at 06:53:59 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: 257 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3000 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: 2.700197 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): -15.30400 44.02500 ymin,ymax (A): 19.34800 76.92400 zmin,zma (A): -69.20700 -20.10600 x,y,z range (A): 59.32900 57.57600 49.10100 scale (grids/A): 2.700197 object centre (A): 14.36050 48.13600 -44.65650 number of atom coordinates read : 3000 total number of charged atoms : 2839 net assigned charge : -6.499979 assigned positive charge : 434.6584 centred at (gu) : 87.39941 89.57156 87.73219 assigned negative charge : -441.1590 centred at (gu) : 87.24387 90.75645 87.73830 start vw surface at 0.1700000 fill in re-entrant regions at 0.5900000 boundary points on vw surface= 174984 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25843 grid for indexing accessible points = 1.400000 m= 84745 mr = 125954 m= 29449 mr = 67911 m= 6588 mr = 22972 m= 777 mr = 4685 m= 28 mr = 463 m= 0 mr = 9 time to grow re-entrant surface = 1.030000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.730000 number of dielectric boundary points 74577 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.890000 number of grid points assigned charge 22708 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) : 1.800131 object centre at (A) : 14.36050 48.13600 -44.65650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1501734 0.3029655 midg,1,midg; midg,igrid,midg 4.6927892E-02 -0.3175631 1,midg,midg; igrid,midg,midg -0.4539566 -0.5956216 gauss-seidel spectral radius is 0.9992406 estimated iterations to convergence 286 setup time was (sec) 2.070000 now iterating at: 06:54:02 rms-change max change #iterations 10.01640 343.3159 at 10iterations 5.877630 198.7416 at 20iterations 3.413383 67.36390 at 30iterations 1.976509 37.54642 at 40iterations 1.137429 25.89527 at 50iterations 0.6534182 13.01475 at 60iterations 0.3741721 7.798963 at 70iterations 0.2147004 4.510631 at 80iterations 0.1224911 2.395309 at 90iterations 7.0165731E-02 1.289341 at 100iterations 3.9929770E-02 0.7717171 at 110iterations 2.2847746E-02 0.4315033 at 120iterations 1.3020687E-02 0.2277122 at 130iterations 7.4277790E-03 0.1266670 at 140iterations 4.2401878E-03 8.6082458E-02 at 150iterations 2.4169881E-03 4.0489197E-02 at 160iterations 1.3779958E-03 2.5325775E-02 at 170iterations 7.8624778E-04 1.4650345E-02 at 180iterations finished qdiffx linear iterations at : 06:54:16 total time elapsed so far: 16.00000 # loops : 180 mean,max change (kT/e) : 7.8624778E-04 1.4650345E-02 energy calculations done at 16.00000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.18000 DelPhi exited at 06:54:16 16.177u 0.326s 0:16.93 97.4% 0+0k 0+0io 0pf+0w