Mon Oct 10 09:44:05 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 Mon Oct 10 2011 at 09:44:05 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 = 2925 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: 0.5789654 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): -16.93800 36.11500 ymin,ymax (A): -64.34000 -4.700000 zmin,zma (A): -4.697000 56.79200 x,y,z range (A): 53.05300 59.64000 61.48900 scale (grids/A): 0.5789654 object centre (A): 9.588499 -34.52000 26.04750 number of atom coordinates read : 2925 total number of charged atoms : 2770 net assigned charge : 6.000019 assigned positive charge : 428.1438 centred at (gu) : 89.48946 89.27639 87.69063 assigned negative charge : -422.1442 centred at (gu) : 89.61294 89.24062 87.47429 start vw surface at 0.1800000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 6546 nv = 96 ne = 84 npr = 56989 no. pairs analyzed = 56989 no. exposed pairs = 4469 no. arc points = 31810 no. surface atoms = 1479 nbur = 1446 mkacc time = 0.1300000 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 = 1.512000 m= 328 mr = 2819 m= 4 mr = 12 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3500000 number of dielectric boundary points 4047 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3127 ## 341 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 8300 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.4559304E-09 3.2667133E-09 midg,1,midg; midg,igrid,midg 7.5719991E-10 1.7606391E-09 1,midg,midg; igrid,midg,midg 4.2899311E-09 -1.0053223E-09 gauss-seidel spectral radius is 0.9846162 estimated iterations to convergence 66 setup time was (sec) 0.5900000 now iterating at: 09:44:06 rms-change max change #iterations 9.5325552E-02 15.85656 at 10iterations 7.4469410E-03 1.178204 at 20iterations 5.8044499E-04 0.1077957 at 30iterations 5.3484557E-05 7.8277588E-03 at 40iterations 7.2627454E-06 9.9372864E-04 at 50iterations finished qdiffx linear iterations at : 09:44:09 total time elapsed so far: 3.350000 # loops : 50 mean,max change (kT/e) : 7.2627454E-06 9.9372864E-04 energy calculations done at 3.350000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.540000 DelPhi exited at 09:44:09 3.549u 0.144s 0:04.04 91.0% 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 Mon Oct 10 2011 at 09:44:09 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 = 2925 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: 1.736896 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): -16.93800 36.11500 ymin,ymax (A): -64.34000 -4.700000 zmin,zma (A): -4.697000 56.79200 x,y,z range (A): 53.05300 59.64000 61.48900 scale (grids/A): 1.736896 object centre (A): 9.588499 -34.52000 26.04750 number of atom coordinates read : 2925 total number of charged atoms : 2770 net assigned charge : 6.000019 assigned positive charge : 428.1438 centred at (gu) : 88.46770 87.82882 83.07155 assigned negative charge : -422.1442 centred at (gu) : 88.83868 87.72125 82.42263 start vw surface at 0.1500000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 70346 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31810 grid for indexing accessible points = 1.400000 m= 21779 mr = 42756 m= 2652 mr = 13533 m= 112 mr = 1080 m= 4 mr = 15 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5400000 number of dielectric boundary points 37509 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 227 iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 21517 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) : 0.5789654 object centre at (A) : 9.588499 -34.52000 26.04750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.5724590E-02 2.4033777E-02 midg,1,midg; midg,igrid,midg 2.2667225E-02 3.0570967E-02 1,midg,midg; igrid,midg,midg 1.5383710E-02 7.3280935E-03 gauss-seidel spectral radius is 0.9984168 estimated iterations to convergence 199 setup time was (sec) 0.8400000 now iterating at: 09:44:10 rms-change max change #iterations 3.699201 167.6776 at 10iterations 1.629237 57.06693 at 20iterations 0.7177128 27.68435 at 30iterations 0.3147124 10.88394 at 40iterations 0.1391064 4.583485 at 50iterations 6.1329968E-02 2.383614 at 60iterations 2.6944235E-02 0.9801006 at 70iterations 1.1861987E-02 0.3805580 at 80iterations 5.2476213E-03 0.1860542 at 90iterations 2.3201848E-03 7.9423904E-02 at 100iterations 1.0213333E-03 3.8087845E-02 at 110iterations 4.5237871E-04 1.5732765E-02 at 120iterations finished qdiffx linear iterations at : 09:44:17 total time elapsed so far: 7.740000 # loops : 120 mean,max change (kT/e) : 4.5237871E-04 1.5732765E-02 energy calculations done at 7.740000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.940000 DelPhi exited at 09:44:18 7.941u 0.220s 0:08.45 96.5% 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 09:44:18 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 = 2925 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: 2.605344 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): -16.93800 36.11500 ymin,ymax (A): -64.34000 -4.700000 zmin,zma (A): -4.697000 56.79200 x,y,z range (A): 53.05300 59.64000 61.48900 scale (grids/A): 2.605344 object centre (A): 9.588499 -34.52000 26.04750 number of atom coordinates read : 2925 total number of charged atoms : 2770 net assigned charge : 6.000019 assigned positive charge : 428.1438 centred at (gu) : 87.70138 86.74294 79.60712 assigned negative charge : -422.1442 centred at (gu) : 88.25780 86.58185 78.63383 start vw surface at 0.1900000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 162785 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31810 grid for indexing accessible points = 1.400000 m= 72027 mr = 106113 m= 22771 mr = 53144 m= 4120 mr = 15808 m= 333 mr = 2355 m= 8 mr = 123 m= 0 mr = 2 time to grow re-entrant surface = 0.7700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.370000 number of dielectric boundary points 84499 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 1.520000 number of grid points assigned charge 22150 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) : 1.736896 object centre at (A) : 9.588499 -34.52000 26.04750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3858060 0.3261780 midg,1,midg; midg,igrid,midg 0.6037006 0.4379945 1,midg,midg; igrid,midg,midg 0.1586268 0.1235827 gauss-seidel spectral radius is 0.9992263 estimated iterations to convergence 284 setup time was (sec) 1.700000 now iterating at: 09:44:20 rms-change max change #iterations 9.479355 295.2345 at 10iterations 5.600146 158.6283 at 20iterations 3.261151 76.98195 at 30iterations 1.889084 50.98864 at 40iterations 1.088443 28.42983 at 50iterations 0.6244164 16.38844 at 60iterations 0.3579985 10.31225 at 70iterations 0.2045857 5.339989 at 80iterations 0.1168946 2.527103 at 90iterations 6.6606559E-02 1.457258 at 100iterations 3.8009953E-02 0.8085737 at 110iterations 2.1574136E-02 0.4845734 at 120iterations 1.2294835E-02 0.2760019 at 130iterations 6.9697746E-03 0.1485963 at 140iterations 3.9706929E-03 8.8844299E-02 at 150iterations 2.2534181E-03 4.8472404E-02 at 160iterations 1.2806518E-03 3.2122612E-02 at 170iterations 7.2754105E-04 1.4161110E-02 at 180iterations finished qdiffx linear iterations at : 09:44:31 total time elapsed so far: 12.95000 # loops : 180 mean,max change (kT/e) : 7.2754105E-04 1.4161110E-02 energy calculations done at 12.95000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.14000 DelPhi exited at 09:44:31 13.144u 0.181s 0:13.62 97.7% 0+0k 0+0io 0pf+0w