Sun Oct 9 08:27:44 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 Sun Oct 9 2011 at 08:27:44 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5811 !!! WARNING: HIR 702 has a net charge of 0.5140 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: 0.4803022 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): 3.918000 78.03800 ymin,ymax (A): 21.94200 84.07100 zmin,zma (A): 6.700000 72.11500 x,y,z range (A): 74.12000 62.12900 65.41500 scale (grids/A): 0.4803022 object centre (A): 40.97800 53.00650 39.40750 number of atom coordinates read : 5811 total number of charged atoms : 5645 net assigned charge : 1.514050 assigned positive charge : 876.4284 centred at (gu) : 89.47914 88.92629 89.14764 assigned negative charge : -874.9218 centred at (gu) : 89.32037 88.91970 89.06457 start vw surface at 0.1500000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 8274 nv = 96 ne = 84 npr = 117075 no. pairs analyzed = 117075 no. exposed pairs = 7288 no. arc points = 50471 no. surface atoms = 2442 nbur = 3369 mkacc time = 0.2100000 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 = 1.792000 m= 270 mr = 4181 m= 1 mr = 10 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3900000 number of dielectric boundary points 4354 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4756 ## 820 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 11292 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -7.7271342E-11 5.6947187E-11 midg,1,midg; midg,igrid,midg 1.7983895E-12 8.8705796E-12 1,midg,midg; igrid,midg,midg -1.4294735E-10 1.1301823E-10 gauss-seidel spectral radius is 0.9779175 estimated iterations to convergence 56 setup time was (sec) 0.5700000 now iterating at: 08:27:45 rms-change max change #iterations 5.4716885E-02 9.924107 at 10iterations 2.7078353E-03 0.4085016 at 20iterations 2.6212248E-04 5.8784485E-02 at 30iterations 5.8113055E-05 1.3549805E-02 at 40iterations 1.5567897E-05 3.3779144E-03 at 50iterations finished qdiffx linear iterations at : 08:27:48 total time elapsed so far: 3.420000 # loops : 50 mean,max change (kT/e) : 1.5567897E-05 3.3779144E-03 energy calculations done at 3.420000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.540000 DelPhi exited at 08:27:48 3.546u 0.169s 0:03.99 92.7% 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 Sun Oct 9 2011 at 08:27:49 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5811 !!! WARNING: HIR 702 has a net charge of 0.5140 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: 1.440907 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): 3.918000 78.03800 ymin,ymax (A): 21.94200 84.07100 zmin,zma (A): 6.700000 72.11500 x,y,z range (A): 74.12000 62.12900 65.41500 scale (grids/A): 1.440907 object centre (A): 40.97800 53.00650 39.40750 number of atom coordinates read : 5811 total number of charged atoms : 5645 net assigned charge : 1.514050 assigned positive charge : 876.4284 centred at (gu) : 88.43590 86.77690 87.44112 assigned negative charge : -874.9218 centred at (gu) : 87.96053 86.75877 87.19352 start vw surface at 0.1400000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 94899 reading accessible surface arcs data from file ARCDAT no. of arc points read = 50471 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.680000 m= 25070 mr = 64589 m= 1660 mr = 15742 m= 19 mr = 578 m= 0 mr = 2 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 651 time to turn everything in is 0.4600000 number of dielectric boundary points 40737 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 817 ## 16 charges are in solution ## iepsmp to db, and charging done at 0.5400000 number of grid points assigned charge 41308 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) : 0.4803022 object centre at (A) : 40.97800 53.00650 39.40750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.7747094E-03 4.0335325E-03 midg,1,midg; midg,igrid,midg -1.0589440E-03 -2.6248123E-03 1,midg,midg; igrid,midg,midg -5.6084022E-03 2.1529282E-02 gauss-seidel spectral radius is 0.9979297 estimated iterations to convergence 175 setup time was (sec) 0.6700000 now iterating at: 08:27:49 rms-change max change #iterations 3.669988 150.4396 at 10iterations 1.437294 52.67651 at 20iterations 0.5665511 18.28107 at 30iterations 0.2230068 7.486214 at 40iterations 8.7488353E-02 2.749584 at 50iterations 3.4672197E-02 1.176880 at 60iterations 1.3677094E-02 0.5225129 at 70iterations 5.4185619E-03 0.1913235 at 80iterations 2.1474198E-03 6.7602158E-02 at 90iterations 8.6220936E-04 2.8648376E-02 at 100iterations 3.5387781E-04 1.3351440E-02 at 110iterations 1.5384599E-04 5.9914589E-03 at 120iterations finished qdiffx linear iterations at : 08:27:56 total time elapsed so far: 7.650000 # loops : 120 mean,max change (kT/e) : 1.5384599E-04 5.9914589E-03 energy calculations done at 7.650000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.790000 DelPhi exited at 08:27:57 7.789u 0.197s 0:08.30 96.0% 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 Sun Oct 9 2011 at 08:27:57 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5811 !!! WARNING: HIR 702 has a net charge of 0.5140 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: 2.161360 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): 3.918000 78.03800 ymin,ymax (A): 21.94200 84.07100 zmin,zma (A): 6.700000 72.11500 x,y,z range (A): 74.12000 62.12900 65.41500 scale (grids/A): 2.161360 object centre (A): 40.97800 53.00650 39.40750 number of atom coordinates read : 5811 total number of charged atoms : 5645 net assigned charge : 1.514050 assigned positive charge : 876.4284 centred at (gu) : 87.65345 85.16496 86.16105 assigned negative charge : -874.9218 centred at (gu) : 86.94078 85.13803 85.79012 start vw surface at 0.1400000 fill in re-entrant regions at 0.3800000 boundary points on vw surface= 222140 reading accessible surface arcs data from file ARCDAT no. of arc points read = 50471 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.652000 m= 93520 mr = 160095 m= 20042 mr = 70922 m= 2063 mr = 13647 m= 69 mr = 1109 m= 0 mr = 21 time to grow re-entrant surface = 0.6200001 no. cavity mid-points inaccessible to solvent = 2277 time to turn everything in is 1.090000 number of dielectric boundary points 92040 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 118 iepsmp to db, and charging done at 1.190000 number of grid points assigned charge 44909 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) : 1.440907 object centre at (A) : 40.97800 53.00650 39.40750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1721030 2.1351598E-02 midg,1,midg; midg,igrid,midg -1.9810751E-02 -3.0167399E-02 1,midg,midg; igrid,midg,midg 4.8088141E-02 0.3644177 gauss-seidel spectral radius is 0.9991347 estimated iterations to convergence 269 setup time was (sec) 1.330000 now iterating at: 08:27:58 rms-change max change #iterations 10.45211 288.1158 at 10iterations 5.973573 153.3804 at 20iterations 3.388145 74.23115 at 30iterations 1.909278 39.28000 at 40iterations 1.072607 24.05903 at 50iterations 0.6005569 13.93031 at 60iterations 0.3349198 6.858341 at 70iterations 0.1865475 3.789591 at 80iterations 0.1036853 2.174892 at 90iterations 5.7600193E-02 1.041008 at 100iterations 3.1834953E-02 0.6937561 at 110iterations 1.7639047E-02 0.3565807 at 120iterations 9.7398423E-03 0.1853294 at 130iterations 5.3946874E-03 0.1100998 at 140iterations 2.9894651E-03 5.8879852E-02 at 150iterations 1.6512764E-03 3.1767845E-02 at 160iterations 9.1409520E-04 1.7990112E-02 at 170iterations 5.0767261E-04 9.6349716E-03 at 180iterations finished qdiffx linear iterations at : 08:28:10 total time elapsed so far: 12.77000 # loops : 180 mean,max change (kT/e) : 5.0767261E-04 9.6349716E-03 energy calculations done at 12.77000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.90000 DelPhi exited at 08:28:10 12.907u 0.208s 0:13.38 97.9% 0+0k 0+0io 0pf+0w