Sun Oct 9 19:15:36 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 Sun Oct 9 2011 at 19:15:37 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4857 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 0.5718783 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): 3.232000 64.60300 ymin,ymax (A): -8.456000 52.69700 zmin,zma (A): -0.8960000 61.35500 x,y,z range (A): 61.37100 61.15300 62.25100 scale (grids/A): 0.5718783 object centre (A): 33.91750 22.12050 30.22950 number of atom coordinates read : 4857 total number of charged atoms : 4717 net assigned charge : 1.121038 assigned positive charge : 745.6912 centred at (gu) : 88.09236 89.26775 89.10938 assigned negative charge : -744.5756 centred at (gu) : 87.96792 89.26877 89.05627 start vw surface at 0.1900000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 10412 nv = 96 ne = 84 npr = 98217 no. pairs analyzed = 98217 no. exposed pairs = 5735 no. arc points = 38745 no. surface atoms = 1943 nbur = 2914 mkacc time = 0.2000000 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 = 1.484000 m= 516 mr = 6015 m= 3 mr = 26 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4400000 number of dielectric boundary points 4890 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3948 ## 403 charges are in solution ## iepsmp to db, and charging done at 0.5600000 number of grid points assigned charge 13545 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.5127575E-09 1.4108927E-09 midg,1,midg; midg,igrid,midg 3.5931999E-10 2.0707347E-10 1,midg,midg; igrid,midg,midg -5.1862408E-09 2.3449305E-09 gauss-seidel spectral radius is 0.9843624 estimated iterations to convergence 66 setup time was (sec) 0.6700000 now iterating at: 19:15:37 rms-change max change #iterations 0.1236671 14.50570 at 10iterations 1.1668199E-02 1.758469 at 20iterations 2.9684766E-03 0.3220825 at 30iterations 1.3497055E-03 0.1448345 at 40iterations 6.5530592E-04 7.9041481E-02 at 50iterations finished qdiffx linear iterations at : 19:15:40 total time elapsed so far: 3.080000 # loops : 50 mean,max change (kT/e) : 6.5530592E-04 7.9041481E-02 energy calculations done at 3.080000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.250000 DelPhi exited at 19:15:40 3.255u 0.143s 0:03.69 91.8% 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 19:15:40 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4857 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.715635 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): 3.232000 64.60300 ymin,ymax (A): -8.456000 52.69700 zmin,zma (A): -0.8960000 61.35500 x,y,z range (A): 61.37100 61.15300 62.25100 scale (grids/A): 1.715635 object centre (A): 33.91750 22.12050 30.22950 number of atom coordinates read : 4857 total number of charged atoms : 4717 net assigned charge : 1.121038 assigned positive charge : 745.6912 centred at (gu) : 84.27589 87.80178 87.32651 assigned negative charge : -744.5756 centred at (gu) : 83.90382 87.80614 87.16872 start vw surface at 0.1900000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 115663 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38745 grid for indexing accessible points = 1.400000 m= 42368 mr = 84009 m= 5814 mr = 30985 m= 230 mr = 3418 m= 1 mr = 36 m= 0 mr = 0 time to grow re-entrant surface = 0.3700000 no. cavity mid-points inaccessible to solvent = 187 time to turn everything in is 0.7500000 number of dielectric boundary points 45628 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 333 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.8700000 number of grid points assigned charge 36519 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) : 0.5718783 object centre at (A) : 33.91750 22.12050 30.22950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.5650216E-02 -3.4938143E-03 midg,1,midg; midg,igrid,midg 1.7752910E-02 9.9397302E-03 1,midg,midg; igrid,midg,midg -2.8150719E-02 4.2828377E-02 gauss-seidel spectral radius is 0.9985318 estimated iterations to convergence 207 setup time was (sec) 1.010000 now iterating at: 19:15:41 rms-change max change #iterations 5.045874 207.9148 at 10iterations 2.288040 66.44513 at 20iterations 1.047444 30.42049 at 30iterations 0.4776230 12.72865 at 40iterations 0.2183607 5.675663 at 50iterations 0.1002127 2.712958 at 60iterations 4.6620049E-02 1.249741 at 70iterations 2.1982979E-02 0.6438980 at 80iterations 1.0942950E-02 0.2996368 at 90iterations 6.1050877E-03 0.1754456 at 100iterations 3.8806293E-03 0.1095543 at 110iterations 2.7322809E-03 7.0178986E-02 at 120iterations finished qdiffx linear iterations at : 19:15:47 total time elapsed so far: 7.070000 # loops : 120 mean,max change (kT/e) : 2.7322809E-03 7.0178986E-02 energy calculations done at 7.070000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.240000 DelPhi exited at 19:15:48 7.244u 0.173s 0:07.67 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 19:15:48 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4857 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 2.573452 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): 3.232000 64.60300 ymin,ymax (A): -8.456000 52.69700 zmin,zma (A): -0.8960000 61.35500 x,y,z range (A): 61.37100 61.15300 62.25100 scale (grids/A): 2.573452 object centre (A): 33.91750 22.12050 30.22950 number of atom coordinates read : 4857 total number of charged atoms : 4717 net assigned charge : 1.121038 assigned positive charge : 745.6912 centred at (gu) : 81.41349 86.70229 85.98970 assigned negative charge : -744.5756 centred at (gu) : 80.85573 86.70899 85.75317 start vw surface at 0.1800000 fill in re-entrant regions at 0.5900000 boundary points on vw surface= 268530 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38745 grid for indexing accessible points = 1.400000 m= 139777 mr = 203935 m= 48059 mr = 114694 m= 9970 mr = 37999 m= 1038 mr = 7152 m= 37 mr = 611 m= 0 mr = 2 time to grow re-entrant surface = 1.170000 no. cavity mid-points inaccessible to solvent = 681 time to turn everything in is 1.890000 number of dielectric boundary points 103018 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 11 iepsmp to db, and charging done at 2.020000 number of grid points assigned charge 37716 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) : 1.715635 object centre at (A) : 33.91750 22.12050 30.22950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.5496137 5.0174356E-02 midg,1,midg; midg,igrid,midg -1.0453471E-02 -2.0658536E-02 1,midg,midg; igrid,midg,midg -0.4863054 0.7001384 gauss-seidel spectral radius is 0.9992784 estimated iterations to convergence 294 setup time was (sec) 2.170000 now iterating at: 19:15:50 rms-change max change #iterations 12.51658 332.4539 at 10iterations 7.428390 150.1252 at 20iterations 4.384554 80.93015 at 30iterations 2.578056 51.42880 at 40iterations 1.511832 27.07204 at 50iterations 0.8825909 14.79686 at 60iterations 0.5155785 8.118610 at 70iterations 0.3005445 4.844543 at 80iterations 0.1749868 2.725029 at 90iterations 0.1018438 1.633727 at 100iterations 5.9326865E-02 0.9581356 at 110iterations 3.4736961E-02 0.5289516 at 120iterations 2.0446448E-02 0.3055706 at 130iterations 1.2238310E-02 0.1958008 at 140iterations 7.5549679E-03 0.1397934 at 150iterations 4.9053668E-03 7.7227592E-02 at 160iterations 3.4140262E-03 5.6285858E-02 at 170iterations 2.5494955E-03 4.0708542E-02 at 180iterations finished qdiffx linear iterations at : 19:16:01 total time elapsed so far: 12.88000 # loops : 180 mean,max change (kT/e) : 2.5494955E-03 4.0708542E-02 energy calculations done at 12.88000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.05000 DelPhi exited at 19:16:02 13.050u 0.187s 0:13.55 97.6% 0+0k 0+0io 0pf+0w