Mon Oct 10 14:24:04 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 Mon Oct 10 2011 at 14:24:04 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: 248 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2429 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: 0.6040861 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): -26.43600 22.86400 ymin,ymax (A): -24.02400 34.90800 zmin,zma (A): -37.04600 14.53900 x,y,z range (A): 49.30000 58.93200 51.58500 scale (grids/A): 0.6040861 object centre (A): -1.785999 5.441998 -11.25350 number of atom coordinates read : 2429 total number of charged atoms : 2272 net assigned charge : 6.3031912E-06 assigned positive charge : 355.1722 centred at (gu) : 89.75320 90.41159 89.94616 assigned negative charge : -355.1725 centred at (gu) : 89.58693 90.24949 89.91251 start vw surface at 0.1600000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 5998 nv = 96 ne = 84 npr = 48436 no. pairs analyzed = 48436 no. exposed pairs = 3287 no. arc points = 23314 no. surface atoms = 1104 nbur = 1325 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 292 mr = 3042 m= 0 mr = 15 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 11 time to turn everything in is 0.2800000 number of dielectric boundary points 3233 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2336 ## 258 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 7340 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.2946700E-09 1.2559950E-09 midg,1,midg; midg,igrid,midg -5.6925402E-09 6.6300627E-09 1,midg,midg; igrid,midg,midg -6.7967307E-09 5.8425353E-09 gauss-seidel spectral radius is 0.9858089 estimated iterations to convergence 69 setup time was (sec) 0.5000000 now iterating at: 14:24:05 rms-change max change #iterations 0.1018053 17.16042 at 10iterations 8.7463195E-03 1.310699 at 20iterations 7.4609410E-04 0.1143494 at 30iterations 6.4430620E-05 1.1181355E-02 at 40iterations 5.5381715E-06 8.2874298E-04 at 50iterations finished qdiffx linear iterations at : 14:24:08 total time elapsed so far: 3.150000 # loops : 50 mean,max change (kT/e) : 5.5381715E-06 8.2874298E-04 energy calculations done at 3.150000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.330000 DelPhi exited at 14:24:08 3.329u 0.156s 0:04.05 85.6% 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 Mon Oct 10 2011 at 14:24:08 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: 248 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2429 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: 1.812258 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): -26.43600 22.86400 ymin,ymax (A): -24.02400 34.90800 zmin,zma (A): -37.04600 14.53900 x,y,z range (A): 49.30000 58.93200 51.58500 scale (grids/A): 1.812258 object centre (A): -1.785999 5.441998 -11.25350 number of atom coordinates read : 2429 total number of charged atoms : 2272 net assigned charge : 6.3031912E-06 assigned positive charge : 355.1722 centred at (gu) : 89.25908 91.23441 89.83790 assigned negative charge : -355.1725 centred at (gu) : 88.76054 90.74842 89.73732 start vw surface at 0.1400000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 65191 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23314 grid for indexing accessible points = 1.400000 m= 21774 mr = 43270 m= 2694 mr = 15032 m= 116 mr = 1352 m= 0 mr = 35 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 759 time to turn everything in is 0.5500000 number of dielectric boundary points 30086 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 176 iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 17744 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) : 0.6040861 object centre at (A) : -1.785999 5.441998 -11.25350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.4575426E-03 3.5642188E-03 midg,1,midg; midg,igrid,midg 1.0480845E-03 1.0688358E-02 1,midg,midg; igrid,midg,midg -1.7031718E-02 6.6869766E-03 gauss-seidel spectral radius is 0.9984860 estimated iterations to convergence 204 setup time was (sec) 0.8700000 now iterating at: 14:24:09 rms-change max change #iterations 3.637548 170.2693 at 10iterations 1.616888 66.52125 at 20iterations 0.7283154 30.85240 at 30iterations 0.3252654 11.13656 at 40iterations 0.1461960 5.200234 at 50iterations 6.5712810E-02 2.261129 at 60iterations 2.9448578E-02 1.026055 at 70iterations 1.3275739E-02 0.4849281 at 80iterations 5.9240805E-03 0.2333393 at 90iterations 2.6811215E-03 0.1000748 at 100iterations 1.2041359E-03 4.2874038E-02 at 110iterations 5.3806021E-04 1.8119812E-02 at 120iterations finished qdiffx linear iterations at : 14:24:16 total time elapsed so far: 7.260000 # loops : 120 mean,max change (kT/e) : 5.3806021E-04 1.8119812E-02 energy calculations done at 7.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.440000 DelPhi exited at 14:24:17 7.440u 0.221s 0:08.22 93.1% 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 Mon Oct 10 2011 at 14:24:17 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: 248 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2429 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: 2.718387 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): -26.43600 22.86400 ymin,ymax (A): -24.02400 34.90800 zmin,zma (A): -37.04600 14.53900 x,y,z range (A): 49.30000 58.93200 51.58500 scale (grids/A): 2.718387 object centre (A): -1.785999 5.441998 -11.25350 number of atom coordinates read : 2429 total number of charged atoms : 2272 net assigned charge : 6.3031912E-06 assigned positive charge : 355.1722 centred at (gu) : 88.88847 91.85152 89.75684 assigned negative charge : -355.1725 centred at (gu) : 88.14076 91.12253 89.60589 start vw surface at 0.2200000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 150983 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23314 grid for indexing accessible points = 1.400000 m= 72188 mr = 105715 m= 23368 mr = 57193 m= 4435 mr = 17551 m= 474 mr = 2897 m= 25 mr = 266 m= 0 mr = 9 time to grow re-entrant surface = 0.7000000 no. cavity mid-points inaccessible to solvent = 2482 time to turn everything in is 1.290000 number of dielectric boundary points 67842 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.420000 number of grid points assigned charge 18174 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) : 1.812258 object centre at (A) : -1.785999 5.441998 -11.25350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1818808 6.7744255E-02 midg,1,midg; midg,igrid,midg 8.5237183E-02 3.7519233E-03 1,midg,midg; igrid,midg,midg -0.2123243 5.0368875E-02 gauss-seidel spectral radius is 0.9992228 estimated iterations to convergence 283 setup time was (sec) 1.600000 now iterating at: 14:24:18 rms-change max change #iterations 8.907720 323.2469 at 10iterations 5.199875 123.0070 at 20iterations 2.995239 76.93852 at 30iterations 1.723551 43.20864 at 40iterations 0.9831706 22.75217 at 50iterations 0.5623209 12.37016 at 60iterations 0.3202924 6.428157 at 70iterations 0.1827840 3.814140 at 80iterations 0.1039069 2.245332 at 90iterations 5.8986992E-02 1.129112 at 100iterations 3.3560738E-02 0.7047882 at 110iterations 1.8996254E-02 0.3789854 at 120iterations 1.0788276E-02 0.2360936 at 130iterations 6.1066411E-03 0.1214027 at 140iterations 3.4669091E-03 6.9599152E-02 at 150iterations 1.9618024E-03 4.1433334E-02 at 160iterations 1.1117994E-03 2.3043871E-02 at 170iterations 6.2957348E-04 1.4822960E-02 at 180iterations finished qdiffx linear iterations at : 14:24:30 total time elapsed so far: 12.72000 # loops : 180 mean,max change (kT/e) : 6.2957348E-04 1.4822960E-02 energy calculations done at 12.72000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.96000 DelPhi exited at 14:24:30 12.964u 0.250s 0:13.62 96.9% 0+0k 0+0io 0pf+0w