Tue Oct 11 08:22:17 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 08:22:17 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 = 2717 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5762942 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): -18.61000 34.13500 ymin,ymax (A): 38.36700 100.1410 zmin,zma (A): -16.99800 39.80700 x,y,z range (A): 52.74500 61.77400 56.80500 scale (grids/A): 0.5762942 object centre (A): 7.762500 69.25400 11.40450 number of atom coordinates read : 2717 total number of charged atoms : 2570 net assigned charge : 6.500021 assigned positive charge : 413.9698 centred at (gu) : 92.51534 91.91297 90.15034 assigned negative charge : -407.4707 centred at (gu) : 92.56986 91.84480 90.22419 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 5833 nv = 96 ne = 84 npr = 54821 no. pairs analyzed = 54821 no. exposed pairs = 3431 no. arc points = 24246 no. surface atoms = 1151 nbur = 1566 mkacc time = 8.9999996E-02 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= 231 mr = 3022 m= 0 mr = 10 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2000000 number of dielectric boundary points 3032 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2485 ## 295 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 7516 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.4390188E-09 -7.9874017E-11 midg,1,midg; midg,igrid,midg 3.4690310E-11 3.8168815E-09 1,midg,midg; igrid,midg,midg 1.2299544E-09 4.3068329E-10 gauss-seidel spectral radius is 0.9844364 estimated iterations to convergence 66 setup time was (sec) 0.3800000 now iterating at: 08:22:18 rms-change max change #iterations 8.9597568E-02 16.55515 at 10iterations 6.7795562E-03 1.116766 at 20iterations 5.2219885E-04 8.8565826E-02 at 30iterations 4.1497078E-05 6.7024231E-03 at 40iterations 3.2369462E-06 4.7874451E-04 at 50iterations finished qdiffx linear iterations at : 08:22:21 total time elapsed so far: 3.230000 # loops : 50 mean,max change (kT/e) : 3.2369462E-06 4.7874451E-04 energy calculations done at 3.230000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.360000 DelPhi exited at 08:22:21 3.359u 0.178s 0:04.03 87.3% 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 08:22:21 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 = 2717 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.728883 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): -18.61000 34.13500 ymin,ymax (A): 38.36700 100.1410 zmin,zma (A): -16.99800 39.80700 x,y,z range (A): 52.74500 61.77400 56.80500 scale (grids/A): 1.728883 object centre (A): 7.762500 69.25400 11.40450 number of atom coordinates read : 2717 total number of charged atoms : 2570 net assigned charge : 6.500021 assigned positive charge : 413.9698 centred at (gu) : 97.54551 95.73843 90.45079 assigned negative charge : -407.4707 centred at (gu) : 97.70930 95.53431 90.67253 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 64089 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24246 grid for indexing accessible points = 1.400000 m= 19824 mr = 43202 m= 2262 mr = 13827 m= 67 mr = 1149 m= 1 mr = 8 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 553 time to turn everything in is 0.3000000 number of dielectric boundary points 28057 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 236 iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 19894 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) : 0.5762942 object centre at (A) : 7.762500 69.25400 11.40450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.1258329E-02 -1.0823330E-02 midg,1,midg; midg,igrid,midg -1.0625803E-02 1.3511475E-02 1,midg,midg; igrid,midg,midg -1.3468237E-04 -6.9229933E-04 gauss-seidel spectral radius is 0.9983508 estimated iterations to convergence 195 setup time was (sec) 0.5200000 now iterating at: 08:22:22 rms-change max change #iterations 3.557955 154.2836 at 10iterations 1.544322 57.11080 at 20iterations 0.6709436 26.25851 at 30iterations 0.2905605 10.42097 at 40iterations 0.1259585 5.211411 at 50iterations 5.4630898E-02 1.957167 at 60iterations 2.3692265E-02 0.7753296 at 70iterations 1.0339620E-02 0.4660912 at 80iterations 4.4889781E-03 0.1605835 at 90iterations 1.9423099E-03 6.7908287E-02 at 100iterations 8.4734382E-04 2.9998779E-02 at 110iterations 3.6914687E-04 1.2723923E-02 at 120iterations finished qdiffx linear iterations at : 08:22:29 total time elapsed so far: 7.480000 # loops : 120 mean,max change (kT/e) : 3.6914687E-04 1.2723923E-02 energy calculations done at 7.480000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.610000 DelPhi exited at 08:22:30 7.613u 0.213s 0:08.31 94.1% 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 Tue Oct 11 2011 at 08:22:30 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 = 2717 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.593324 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): -18.61000 34.13500 ymin,ymax (A): 38.36700 100.1410 zmin,zma (A): -16.99800 39.80700 x,y,z range (A): 52.74500 61.77400 56.80500 scale (grids/A): 2.593324 object centre (A): 7.762500 69.25400 11.40450 number of atom coordinates read : 2717 total number of charged atoms : 2570 net assigned charge : 6.500021 assigned positive charge : 413.9698 centred at (gu) : 101.3183 98.60764 90.67594 assigned negative charge : -407.4707 centred at (gu) : 101.5640 98.30131 91.00884 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 148844 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24246 grid for indexing accessible points = 1.400000 m= 68499 mr = 105710 m= 19865 mr = 54510 m= 3525 mr = 15045 m= 341 mr = 2400 m= 10 mr = 180 m= 0 mr = 0 time to grow re-entrant surface = 0.4200000 no. cavity mid-points inaccessible to solvent = 1762 time to turn everything in is 0.7800000 number of dielectric boundary points 63239 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 10 iepsmp to db, and charging done at 0.8700000 number of grid points assigned charge 20548 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) : 1.728883 object centre at (A) : 7.762500 69.25400 11.40450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.9410543E-02 -0.2635479 midg,1,midg; midg,igrid,midg -0.1440334 7.0558727E-02 1,midg,midg; igrid,midg,midg -4.6089593E-02 -1.1206562E-02 gauss-seidel spectral radius is 0.9991834 estimated iterations to convergence 276 setup time was (sec) 1.020000 now iterating at: 08:22:31 rms-change max change #iterations 8.885632 318.5570 at 10iterations 5.061983 157.6697 at 20iterations 2.864228 70.86742 at 30iterations 1.618385 40.55681 at 40iterations 0.9095855 21.15411 at 50iterations 0.5102814 11.64077 at 60iterations 0.2865326 6.748736 at 70iterations 0.1602993 3.257343 at 80iterations 8.9827396E-02 1.899225 at 90iterations 5.0157804E-02 1.041424 at 100iterations 2.8032213E-02 0.5680332 at 110iterations 1.5687440E-02 0.3403416 at 120iterations 8.7811677E-03 0.1722336 at 130iterations 4.8932647E-03 9.5520020E-02 at 140iterations 2.7276890E-03 5.8776855E-02 at 150iterations 1.5251178E-03 3.0806065E-02 at 160iterations 8.4908714E-04 1.8521190E-02 at 170iterations 4.7385952E-04 1.0528564E-02 at 180iterations finished qdiffx linear iterations at : 08:22:42 total time elapsed so far: 12.08000 # loops : 180 mean,max change (kT/e) : 4.7385952E-04 1.0528564E-02 energy calculations done at 12.08000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.21000 DelPhi exited at 08:22:42 12.211u 0.208s 0:12.71 97.6% 0+0k 0+0io 0pf+0w