Sat Oct 15 11:28:50 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 Sat Oct 15 2011 at 11:28:50 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3600 !!! WARNING: ASL 227 has a net charge of -0.1000 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: 0.5140126 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): -5.143000 64.11600 ymin,ymax (A): 14.51300 76.14900 zmin,zma (A): -13.38600 34.62200 x,y,z range (A): 69.25900 61.63600 48.00800 scale (grids/A): 0.5140126 object centre (A): 29.48650 45.33100 10.61800 number of atom coordinates read : 3600 total number of charged atoms : 3453 net assigned charge : -8.099985 assigned positive charge : 551.1221 centred at (gu) : 90.05087 87.49561 89.45988 assigned negative charge : -559.2239 centred at (gu) : 90.03011 87.53498 89.48419 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 5946 nv = 96 ne = 84 npr = 73274 no. pairs analyzed = 73274 no. exposed pairs = 4355 no. arc points = 30408 no. surface atoms = 1468 nbur = 2132 mkacc time = 0.1200000 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 = 1.652000 m= 220 mr = 3123 m= 1 mr = 3 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2500000 number of dielectric boundary points 3041 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2994 ## 428 charges are in solution ## iepsmp to db, and charging done at 0.3100000 number of grid points assigned charge 7992 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -9.0442182E-11 -1.6740857E-10 midg,1,midg; midg,igrid,midg -7.9539868E-11 -1.2012791E-10 1,midg,midg; igrid,midg,midg -1.8166030E-10 -8.8444654E-11 gauss-seidel spectral radius is 0.9805527 estimated iterations to convergence 59 setup time was (sec) 0.4300000 now iterating at: 11:28:51 rms-change max change #iterations 6.1924450E-02 12.07476 at 10iterations 3.5580986E-03 0.6084747 at 20iterations 2.2720755E-04 4.2850494E-02 at 30iterations 2.4152338E-05 4.5299530E-03 at 40iterations 4.5472830E-06 9.5558167E-04 at 50iterations finished qdiffx linear iterations at : 11:28:54 total time elapsed so far: 3.320000 # loops : 50 mean,max change (kT/e) : 4.5472830E-06 9.5558167E-04 energy calculations done at 3.320000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.460000 DelPhi exited at 11:28:54 3.462u 0.166s 0:03.92 92.3% 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 Sat Oct 15 2011 at 11:28:54 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3600 !!! WARNING: ASL 227 has a net charge of -0.1000 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: 1.542038 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): -5.143000 64.11600 ymin,ymax (A): 14.51300 76.14900 zmin,zma (A): -13.38600 34.62200 x,y,z range (A): 69.25900 61.63600 48.00800 scale (grids/A): 1.542038 object centre (A): 29.48650 45.33100 10.61800 number of atom coordinates read : 3600 total number of charged atoms : 3453 net assigned charge : -8.099985 assigned positive charge : 551.1221 centred at (gu) : 90.15174 82.48596 88.37874 assigned negative charge : -559.2239 centred at (gu) : 90.08960 82.60442 88.45238 start vw surface at 0.1100000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 67292 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30408 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 19628 mr = 46356 m= 1822 mr = 13391 m= 35 mr = 833 m= 1 mr = 1 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 414 time to turn everything in is 0.3400000 number of dielectric boundary points 28197 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 409 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 26080 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) : 0.5140126 object centre at (A) : 29.48650 45.33100 10.61800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.3218741E-03 -1.6859917E-03 midg,1,midg; midg,igrid,midg -1.5318096E-02 -1.3016162E-02 1,midg,midg; igrid,midg,midg 6.2397807E-03 -3.9680451E-03 gauss-seidel spectral radius is 0.9980035 estimated iterations to convergence 178 setup time was (sec) 0.5500000 now iterating at: 11:28:55 rms-change max change #iterations 3.313387 154.5718 at 10iterations 1.320831 52.04990 at 20iterations 0.5310627 18.62921 at 30iterations 0.2121582 7.848413 at 40iterations 8.4576927E-02 3.152542 at 50iterations 3.3989102E-02 1.104546 at 60iterations 1.3628502E-02 0.5178947 at 70iterations 5.4522753E-03 0.1994505 at 80iterations 2.1793796E-03 7.8279495E-02 at 90iterations 8.7607175E-04 3.3153534E-02 at 100iterations 3.5272146E-04 1.2680054E-02 at 110iterations 1.4266092E-04 4.8894882E-03 at 120iterations finished qdiffx linear iterations at : 11:29:02 total time elapsed so far: 7.560000 # loops : 120 mean,max change (kT/e) : 1.4266092E-04 4.8894882E-03 energy calculations done at 7.560000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.690000 DelPhi exited at 11:29:02 7.693u 0.194s 0:08.15 96.6% 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 Sat Oct 15 2011 at 11:29:02 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3600 !!! WARNING: ASL 227 has a net charge of -0.1000 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: 2.313057 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): -5.143000 64.11600 ymin,ymax (A): 14.51300 76.14900 zmin,zma (A): -13.38600 34.62200 x,y,z range (A): 69.25900 61.63600 48.00800 scale (grids/A): 2.313057 object centre (A): 29.48650 45.33100 10.61800 number of atom coordinates read : 3600 total number of charged atoms : 3453 net assigned charge : -8.099985 assigned positive charge : 551.1221 centred at (gu) : 90.22735 78.72860 87.56806 assigned negative charge : -559.2239 centred at (gu) : 90.13445 78.90653 87.67847 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 156841 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30408 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 70418 mr = 113969 m= 18177 mr = 55448 m= 2649 mr = 13363 m= 123 mr = 1689 m= 1 mr = 31 m= 0 mr = 0 time to grow re-entrant surface = 0.4500000 no. cavity mid-points inaccessible to solvent = 1368 time to turn everything in is 0.8000000 number of dielectric boundary points 63709 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 40 iepsmp to db, and charging done at 0.8800000 number of grid points assigned charge 27546 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) : 1.542038 object centre at (A) : 29.48650 45.33100 10.61800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.1405415E-04 -1.7401189E-02 midg,1,midg; midg,igrid,midg -0.3087635 -0.2508150 1,midg,midg; igrid,midg,midg 0.3777266 -6.4557157E-02 gauss-seidel spectral radius is 0.9990849 estimated iterations to convergence 261 setup time was (sec) 1.040000 now iterating at: 11:29:03 rms-change max change #iterations 8.878211 247.5264 at 10iterations 4.911241 122.7499 at 20iterations 2.692485 68.85503 at 30iterations 1.472921 36.23852 at 40iterations 0.8032765 21.96113 at 50iterations 0.4369528 9.440413 at 60iterations 0.2369051 5.274242 at 70iterations 0.1286130 2.508659 at 80iterations 6.9432370E-02 1.605824 at 90iterations 3.7622392E-02 0.7624550 at 100iterations 2.0312207E-02 0.4255311 at 110iterations 1.1004095E-02 0.2223415 at 120iterations 5.9410064E-03 0.1292515 at 130iterations 3.2184811E-03 6.7324638E-02 at 140iterations 1.7471818E-03 3.6041260E-02 at 150iterations 9.5392263E-04 2.0424604E-02 at 160iterations 5.2637467E-04 1.1543751E-02 at 170iterations 2.9538668E-04 7.5435638E-03 at 180iterations finished qdiffx linear iterations at : 11:29:14 total time elapsed so far: 12.11000 # loops : 180 mean,max change (kT/e) : 2.9538668E-04 7.5435638E-03 energy calculations done at 12.11000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.25000 DelPhi exited at 11:29:15 12.252u 0.202s 0:12.76 97.5% 0+0k 0+0io 0pf+0w