Sun Oct 9 09:36:41 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 Sun Oct 9 2011 at 09:36:41 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2771 !!! WARNING: GLN 1020 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.5603211 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): -80.69500 -33.28800 ymin,ymax (A): -34.93100 27.71200 zmin,zma (A): -55.13800 8.397000 x,y,z range (A): 47.40700 62.64300 63.53500 scale (grids/A): 0.5603211 object centre (A): -56.99150 -3.609500 -23.37050 number of atom coordinates read : 2771 total number of charged atoms : 2627 net assigned charge : 0.7280200 assigned positive charge : 410.2686 centred at (gu) : 89.47730 88.77845 88.94678 assigned negative charge : -409.5414 centred at (gu) : 89.48386 88.96257 88.92831 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 5771 nv = 96 ne = 84 npr = 54606 no. pairs analyzed = 54606 no. exposed pairs = 3871 no. arc points = 27263 no. surface atoms = 1292 nbur = 1479 mkacc time = 0.1600000 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 = 1.540000 m= 260 mr = 2790 m= 1 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3800000 number of dielectric boundary points 3228 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2733 ## 290 charges are in solution ## iepsmp to db, and charging done at 0.5400000 number of grid points assigned charge 7445 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.7626742E-10 1.9066596E-10 midg,1,midg; midg,igrid,midg 2.5830762E-09 -1.3969575E-09 1,midg,midg; igrid,midg,midg 1.3982648E-10 -9.9400939E-12 gauss-seidel spectral radius is 0.9835626 estimated iterations to convergence 64 setup time was (sec) 0.7100000 now iterating at: 09:36:42 rms-change max change #iterations 8.0225706E-02 15.20602 at 10iterations 5.6423778E-03 1.155960 at 20iterations 4.0676081E-04 6.9759369E-02 at 30iterations 2.9683413E-05 5.0177574E-03 at 40iterations 2.2105437E-06 3.6621094E-04 at 50iterations finished qdiffx linear iterations at : 09:36:45 total time elapsed so far: 4.280000 # loops : 50 mean,max change (kT/e) : 2.2105437E-06 3.6621094E-04 energy calculations done at 4.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.460000 DelPhi exited at 09:36:46 4.464u 0.294s 0:05.03 94.4% 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 09:36:46 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2771 !!! WARNING: GLN 1020 has a net charge of -0.2720 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: 1.680963 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): -80.69500 -33.28800 ymin,ymax (A): -34.93100 27.71200 zmin,zma (A): -55.13800 8.397000 x,y,z range (A): 47.40700 62.64300 63.53500 scale (grids/A): 1.680963 object centre (A): -56.99150 -3.609500 -23.37050 number of atom coordinates read : 2771 total number of charged atoms : 2627 net assigned charge : 0.7280200 assigned positive charge : 410.2686 centred at (gu) : 88.43134 86.33511 86.83981 assigned negative charge : -409.5414 centred at (gu) : 88.45133 86.88718 86.78472 start vw surface at 0.1500000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 63183 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27263 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 20137 mr = 41001 m= 2287 mr = 13640 m= 76 mr = 1080 m= 1 mr = 8 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5800000 number of dielectric boundary points 29955 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 252 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 20245 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) : 0.5603211 object centre at (A) : -56.99150 -3.609500 -23.37050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.5125816E-02 3.8418823E-04 midg,1,midg; midg,igrid,midg 2.6924439E-02 -3.4475098E-03 1,midg,midg; igrid,midg,midg 7.6502673E-03 3.4591525E-03 gauss-seidel spectral radius is 0.9982823 estimated iterations to convergence 192 setup time was (sec) 0.9500000 now iterating at: 09:36:47 rms-change max change #iterations 3.387010 159.3552 at 10iterations 1.436319 59.19004 at 20iterations 0.6141940 24.09602 at 30iterations 0.2616427 9.064545 at 40iterations 0.1111889 4.786993 at 50iterations 4.7522888E-02 1.730968 at 60iterations 2.0180944E-02 0.8055420 at 70iterations 8.6151119E-03 0.3541145 at 80iterations 3.6865305E-03 0.1327457 at 90iterations 1.5766924E-03 5.5049419E-02 at 100iterations 6.7022920E-04 2.5382996E-02 at 110iterations 2.8757425E-04 1.1947632E-02 at 120iterations finished qdiffx linear iterations at : 09:36:56 total time elapsed so far: 9.920000 # loops : 120 mean,max change (kT/e) : 2.8757425E-04 1.1947632E-02 energy calculations done at 9.920000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.10000 DelPhi exited at 09:36:57 10.105u 0.338s 0:10.79 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 Sun Oct 9 2011 at 09:36:57 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2771 !!! WARNING: GLN 1020 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.521445 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): -80.69500 -33.28800 ymin,ymax (A): -34.93100 27.71200 zmin,zma (A): -55.13800 8.397000 x,y,z range (A): 47.40700 62.64300 63.53500 scale (grids/A): 2.521445 object centre (A): -56.99150 -3.609500 -23.37050 number of atom coordinates read : 2771 total number of charged atoms : 2627 net assigned charge : 0.7280200 assigned positive charge : 410.2686 centred at (gu) : 87.64680 84.50253 85.25941 assigned negative charge : -409.5414 centred at (gu) : 87.67699 85.33070 85.17713 start vw surface at 0.1700000 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 146603 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27263 grid for indexing accessible points = 1.400000 m= 68129 mr = 100965 m= 20769 mr = 53018 m= 3630 mr = 15446 m= 286 mr = 2207 m= 10 mr = 112 m= 0 mr = 0 time to grow re-entrant surface = 0.6999999 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.320000 number of dielectric boundary points 67679 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 11 iepsmp to db, and charging done at 1.480000 number of grid points assigned charge 21002 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) : 1.680963 object centre at (A) : -56.99150 -3.609500 -23.37050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1898309 -5.5502620E-02 midg,1,midg; midg,igrid,midg 0.4976329 0.1025305 1,midg,midg; igrid,midg,midg 0.1121605 6.6291057E-02 gauss-seidel spectral radius is 0.9991707 estimated iterations to convergence 274 setup time was (sec) 1.690000 now iterating at: 09:36:59 rms-change max change #iterations 8.778401 309.0336 at 10iterations 5.026712 123.5304 at 20iterations 2.859821 73.68388 at 30iterations 1.615863 39.60120 at 40iterations 0.9085816 19.33550 at 50iterations 0.5105498 12.73912 at 60iterations 0.2858674 5.894352 at 70iterations 0.1597950 3.663826 at 80iterations 8.9022167E-02 2.068752 at 90iterations 4.9756382E-02 1.082682 at 100iterations 2.7678650E-02 0.5416641 at 110iterations 1.5392451E-02 0.3485136 at 120iterations 8.5890638E-03 0.1907396 at 130iterations 4.7790953E-03 0.1115608 at 140iterations 2.6579020E-03 5.5110931E-02 at 150iterations 1.4766541E-03 3.1761646E-02 at 160iterations 8.2107284E-04 1.7518997E-02 at 170iterations 4.5698328E-04 9.5748901E-03 at 180iterations finished qdiffx linear iterations at : 09:37:13 total time elapsed so far: 15.97000 # loops : 180 mean,max change (kT/e) : 4.5698328E-04 9.5748901E-03 energy calculations done at 15.97000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.17000 DelPhi exited at 09:37:14 16.170u 0.341s 0:16.79 98.3% 0+0k 0+0io 0pf+0w