Sat Oct 8 20:31:41 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 8 2011 at 20:31:41 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2593 !!! WARNING: GLM 92 has a net charge of -0.0940 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN4 491 has a net charge of 1.4000 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: 0.6161515 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): -30.81900 17.32300 ymin,ymax (A): -23.62500 23.63500 zmin,zma (A): -12.59300 45.18500 x,y,z range (A): 48.14200 47.26000 57.77800 scale (grids/A): 0.6161515 object centre (A): -6.748000 5.0001144E-03 16.29600 number of atom coordinates read : 2593 total number of charged atoms : 2450 net assigned charge : 3.906008 assigned positive charge : 391.8441 centred at (gu) : 88.42267 89.01426 89.71375 assigned negative charge : -387.9385 centred at (gu) : 88.33606 89.05656 89.58939 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6350 nv = 96 ne = 84 npr = 54589 no. pairs analyzed = 54589 no. exposed pairs = 2989 no. arc points = 21491 no. surface atoms = 1005 nbur = 1588 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 336 mr = 3555 m= 3 mr = 25 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 72 time to turn everything in is 0.2000000 number of dielectric boundary points 3109 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2149 ## 201 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 7964 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.8980922E-09 9.5069321E-09 midg,1,midg; midg,igrid,midg 6.6750632E-09 3.1782221E-10 1,midg,midg; igrid,midg,midg -3.3646139E-09 5.6239897E-09 gauss-seidel spectral radius is 0.9863546 estimated iterations to convergence 70 setup time was (sec) 0.3900000 now iterating at: 20:31:41 rms-change max change #iterations 0.1235736 20.95130 at 10iterations 1.1166599E-02 1.636197 at 20iterations 1.0110494E-03 0.1541901 at 30iterations 9.9276331E-05 1.3946533E-02 at 40iterations 9.6701597E-06 1.4381409E-03 at 50iterations finished qdiffx linear iterations at : 20:31:44 total time elapsed so far: 3.270000 # loops : 50 mean,max change (kT/e) : 9.6701597E-06 1.4381409E-03 energy calculations done at 3.270000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.400000 DelPhi exited at 20:31:45 3.404u 0.178s 0:03.87 92.2% 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 8 2011 at 20:31:45 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2593 !!! WARNING: GLM 92 has a net charge of -0.0940 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN4 491 has a net charge of 1.4000 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: 1.848454 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): -30.81900 17.32300 ymin,ymax (A): -23.62500 23.63500 zmin,zma (A): -12.59300 45.18500 x,y,z range (A): 48.14200 47.26000 57.77800 scale (grids/A): 1.848454 object centre (A): -6.748000 5.0001144E-03 16.29600 number of atom coordinates read : 2593 total number of charged atoms : 2450 net assigned charge : 3.906008 assigned positive charge : 391.8441 centred at (gu) : 85.26768 87.04240 89.14088 assigned negative charge : -387.9385 centred at (gu) : 85.00818 87.16933 88.76816 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 69720 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21491 grid for indexing accessible points = 1.400000 m= 23620 mr = 48915 m= 3221 mr = 17303 m= 113 mr = 1859 m= 1 mr = 21 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 2968 time to turn everything in is 0.3500000 number of dielectric boundary points 28577 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 191 iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 19221 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) : 0.6161515 object centre at (A) : -6.748000 5.0001144E-03 16.29600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.9872185E-02 2.4449071E-02 midg,1,midg; midg,igrid,midg 1.2789216E-02 5.3996843E-04 1,midg,midg; igrid,midg,midg -1.1522146E-03 2.7263112E-02 gauss-seidel spectral radius is 0.9985464 estimated iterations to convergence 208 setup time was (sec) 0.5600000 now iterating at: 20:31:46 rms-change max change #iterations 3.970497 163.8212 at 10iterations 1.822483 62.57793 at 20iterations 0.8277542 31.04527 at 30iterations 0.3784509 13.09558 at 40iterations 0.1736841 6.029510 at 50iterations 7.9389028E-02 2.828857 at 60iterations 3.6328759E-02 1.133953 at 70iterations 1.6564822E-02 0.5226622 at 80iterations 7.5832880E-03 0.2464218 at 90iterations 3.4647800E-03 0.1087503 at 100iterations 1.5875101E-03 5.7880402E-02 at 110iterations 7.2904793E-04 2.3332596E-02 at 120iterations finished qdiffx linear iterations at : 20:31:53 total time elapsed so far: 7.630000 # loops : 120 mean,max change (kT/e) : 7.2904793E-04 2.3332596E-02 energy calculations done at 7.630000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.770000 DelPhi exited at 20:31:53 7.774u 0.190s 0:08.24 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 8 2011 at 20:31:53 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2593 !!! WARNING: GLM 92 has a net charge of -0.0940 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN4 491 has a net charge of 1.4000 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: 2.772682 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): -30.81900 17.32300 ymin,ymax (A): -23.62500 23.63500 zmin,zma (A): -12.59300 45.18500 x,y,z range (A): 48.14200 47.26000 57.77800 scale (grids/A): 2.772682 object centre (A): -6.748000 5.0001144E-03 16.29600 number of atom coordinates read : 2593 total number of charged atoms : 2450 net assigned charge : 3.906008 assigned positive charge : 391.8441 centred at (gu) : 82.90144 85.56364 88.71131 assigned negative charge : -387.9385 centred at (gu) : 82.51230 85.75403 88.15225 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 161664 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21491 grid for indexing accessible points = 1.400000 m= 78645 mr = 118468 m= 26018 mr = 64470 m= 5433 mr = 20726 m= 518 mr = 3938 m= 20 mr = 287 m= 1 mr = 4 m= 0 mr = 0 time to grow re-entrant surface = 0.4700000 no. cavity mid-points inaccessible to solvent = 9894 time to turn everything in is 0.8500000 number of dielectric boundary points 64406 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 0.9300000 number of grid points assigned charge 19598 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) : 1.848454 object centre at (A) : -6.748000 5.0001144E-03 16.29600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1147865 0.2727376 midg,1,midg; midg,igrid,midg 0.1427158 -1.5868524E-02 1,midg,midg; igrid,midg,midg 7.6469472E-03 0.3578895 gauss-seidel spectral radius is 0.9992280 estimated iterations to convergence 284 setup time was (sec) 1.080000 now iterating at: 20:31:54 rms-change max change #iterations 9.395256 302.2130 at 10iterations 5.392557 128.3163 at 20iterations 3.074090 62.88992 at 30iterations 1.753240 38.06095 at 40iterations 0.9981014 20.30023 at 50iterations 0.5678649 12.60872 at 60iterations 0.3225691 6.690825 at 70iterations 0.1832354 3.520127 at 80iterations 0.1040118 2.133831 at 90iterations 5.9040036E-02 1.131496 at 100iterations 3.3521522E-02 0.7256966 at 110iterations 1.9025704E-02 0.3553391 at 120iterations 1.0818468E-02 0.2043953 at 130iterations 6.1390437E-03 0.1137924 at 140iterations 3.4890769E-03 6.5850258E-02 at 150iterations 1.9831052E-03 3.6039352E-02 at 160iterations 1.1318204E-03 2.2438049E-02 at 170iterations 6.4395752E-04 1.3280869E-02 at 180iterations finished qdiffx linear iterations at : 20:32:06 total time elapsed so far: 12.38000 # loops : 180 mean,max change (kT/e) : 6.4395752E-04 1.3280869E-02 energy calculations done at 12.38000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.51000 DelPhi exited at 20:32:06 12.512u 0.222s 0:13.03 97.6% 0+0k 0+0io 0pf+0w