Mon Oct 10 14:24:05 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 14:24:05 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 = 2396 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: 0.6043527 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): -24.06900 34.83700 ymin,ymax (A): -14.55000 37.17600 zmin,zma (A): -23.08400 26.32500 x,y,z range (A): 58.90600 51.72600 49.40900 scale (grids/A): 0.6043527 object centre (A): 5.384001 11.31300 1.620501 number of atom coordinates read : 2396 total number of charged atoms : 2239 net assigned charge : -0.9999940 assigned positive charge : 349.0622 centred at (gu) : 90.28152 89.84563 90.38511 assigned negative charge : -350.0625 centred at (gu) : 90.15599 89.90836 90.53408 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 5953 nv = 96 ne = 84 npr = 47646 no. pairs analyzed = 47646 no. exposed pairs = 3321 no. arc points = 23142 no. surface atoms = 1117 nbur = 1279 mkacc time = 0.1600000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 275 mr = 2962 m= 2 mr = 16 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3500000 number of dielectric boundary points 3252 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2322 ## 232 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 7282 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.6069215E-09 -6.7567871E-09 midg,1,midg; midg,igrid,midg 1.9335560E-09 -2.7593228E-09 1,midg,midg; igrid,midg,midg -4.9455848E-09 4.4604032E-09 gauss-seidel spectral radius is 0.9858190 estimated iterations to convergence 69 setup time was (sec) 0.6400000 now iterating at: 14:24:06 rms-change max change #iterations 0.1025054 17.41172 at 10iterations 8.6486293E-03 1.463989 at 20iterations 7.5276714E-04 0.1317081 at 30iterations 6.3408188E-05 1.1198997E-02 at 40iterations 5.5268688E-06 8.3351135E-04 at 50iterations finished qdiffx linear iterations at : 14:24:10 total time elapsed so far: 4.370000 # loops : 50 mean,max change (kT/e) : 5.5268688E-06 8.3351135E-04 energy calculations done at 4.370000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.590000 DelPhi exited at 14:24:10 4.593u 0.463s 0:05.51 91.6% 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 14:24:10 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 = 2396 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: 1.813058 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): -24.06900 34.83700 ymin,ymax (A): -14.55000 37.17600 zmin,zma (A): -23.08400 26.32500 x,y,z range (A): 58.90600 51.72600 49.40900 scale (grids/A): 1.813058 object centre (A): 5.384001 11.31300 1.620501 number of atom coordinates read : 2396 total number of charged atoms : 2239 net assigned charge : -0.9999940 assigned positive charge : 349.0622 centred at (gu) : 90.84409 89.53638 91.15488 assigned negative charge : -350.0625 centred at (gu) : 90.46770 89.72490 91.60194 start vw surface at 0.1500000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 64976 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23142 grid for indexing accessible points = 1.400000 m= 20910 mr = 43038 m= 2542 mr = 14287 m= 103 mr = 1200 m= 1 mr = 16 m= 0 mr = 0 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6700000 number of dielectric boundary points 29991 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 204 iepsmp to db, and charging done at 0.8100000 number of grid points assigned charge 17541 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) : 0.6043527 object centre at (A) : 5.384001 11.31300 1.620501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.7064227E-03 -1.7327322E-02 midg,1,midg; midg,igrid,midg 3.7740448E-03 -9.9138441E-03 1,midg,midg; igrid,midg,midg 1.6311442E-03 1.2513013E-03 gauss-seidel spectral radius is 0.9984854 estimated iterations to convergence 204 setup time was (sec) 1.010000 now iterating at: 14:24:12 rms-change max change #iterations 3.633648 167.9685 at 10iterations 1.624879 73.52036 at 20iterations 0.7310444 26.63550 at 30iterations 0.3269864 11.25437 at 40iterations 0.1472290 5.470356 at 50iterations 6.6379033E-02 2.510196 at 60iterations 2.9731175E-02 0.9545250 at 70iterations 1.3371968E-02 0.4715004 at 80iterations 5.9734811E-03 0.2349825 at 90iterations 2.6894251E-03 9.2304707E-02 at 100iterations 1.2057386E-03 4.5670629E-02 at 110iterations 5.4542487E-04 1.9134521E-02 at 120iterations finished qdiffx linear iterations at : 14:24:21 total time elapsed so far: 10.31000 # loops : 120 mean,max change (kT/e) : 5.4542487E-04 1.9134521E-02 energy calculations done at 10.31000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.53000 DelPhi exited at 14:24:22 10.537u 0.489s 0:11.38 96.7% 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 Mon Oct 10 2011 at 14:24:22 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 = 2396 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: 2.719587 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): -24.06900 34.83700 ymin,ymax (A): -14.55000 37.17600 zmin,zma (A): -23.08400 26.32500 x,y,z range (A): 58.90600 51.72600 49.40900 scale (grids/A): 2.719587 object centre (A): 5.384001 11.31300 1.620501 number of atom coordinates read : 2396 total number of charged atoms : 2239 net assigned charge : -0.9999940 assigned positive charge : 349.0622 centred at (gu) : 91.26600 89.30461 91.73225 assigned negative charge : -350.0625 centred at (gu) : 90.70148 89.58725 92.40293 start vw surface at 0.1600000 fill in re-entrant regions at 0.5700000 boundary points on vw surface= 150611 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23142 grid for indexing accessible points = 1.400000 m= 70832 mr = 105605 m= 21631 mr = 55492 m= 4036 mr = 16009 m= 394 mr = 2499 m= 25 mr = 199 m= 0 mr = 8 time to grow re-entrant surface = 1.050000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.750000 number of dielectric boundary points 67717 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 1.920000 number of grid points assigned charge 17906 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) : 1.813058 object centre at (A) : 5.384001 11.31300 1.620501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.1328074E-02 -0.2442319 midg,1,midg; midg,igrid,midg 6.1381504E-02 -0.1766239 1,midg,midg; igrid,midg,midg 9.7321995E-02 -5.1039562E-02 gauss-seidel spectral radius is 0.9992231 estimated iterations to convergence 283 setup time was (sec) 2.120000 now iterating at: 14:24:24 rms-change max change #iterations 8.920934 309.0833 at 10iterations 5.211748 149.7774 at 20iterations 3.002184 76.55156 at 30iterations 1.729243 42.78478 at 40iterations 0.9926635 21.46124 at 50iterations 0.5677882 14.03656 at 60iterations 0.3234726 8.059621 at 70iterations 0.1844908 4.574757 at 80iterations 0.1050867 2.290313 at 90iterations 5.9617594E-02 1.211355 at 100iterations 3.3821881E-02 0.7131081 at 110iterations 1.9223591E-02 0.4135571 at 120iterations 1.0872948E-02 0.2329693 at 130iterations 6.1875000E-03 0.1216431 at 140iterations 3.5042986E-03 8.1461631E-02 at 150iterations 1.9887623E-03 4.1433334E-02 at 160iterations 1.1257683E-03 2.2086382E-02 at 170iterations 6.3714897E-04 1.3422012E-02 at 180iterations finished qdiffx linear iterations at : 14:24:40 total time elapsed so far: 17.83000 # loops : 180 mean,max change (kT/e) : 6.3714897E-04 1.3422012E-02 energy calculations done at 17.83000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.04000 DelPhi exited at 14:24:41 18.041u 0.490s 0:19.01 97.4% 0+0k 0+0io 0pf+0w