Sat Oct 8 15:58:28 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 Sat Oct 8 2011 at 15:58:28 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: 279 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2339 !!! WARNING: ASL 705 has a net charge of -0.1000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6474140 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): -2.295000 46.29600 ymin,ymax (A): 15.93300 62.52000 zmin,zma (A): -18.56800 36.42000 x,y,z range (A): 48.59100 46.58700 54.98800 scale (grids/A): 0.6474140 object centre (A): 22.00050 39.22650 8.926000 number of atom coordinates read : 2339 total number of charged atoms : 2239 net assigned charge : 2.900002 assigned positive charge : 346.3180 centred at (gu) : 90.28721 88.97793 90.25033 assigned negative charge : -343.4188 centred at (gu) : 90.30766 89.12388 90.32605 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6561 nv = 96 ne = 84 npr = 47944 no. pairs analyzed = 47944 no. exposed pairs = 2868 no. arc points = 19866 no. surface atoms = 977 nbur = 1362 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 343 mr = 3625 m= 1 mr = 56 m= 0 mr = 0 time to grow re-entrant surface = 8.9999989E-02 no. cavity mid-points inaccessible to solvent = 24 time to turn everything in is 0.1900000 number of dielectric boundary points 3224 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1996 ## 189 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 7933 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.3762105E-08 -4.8397388E-09 midg,1,midg; midg,igrid,midg 2.8827076E-08 -1.0890948E-08 1,midg,midg; igrid,midg,midg 7.1790045E-09 2.6057889E-09 gauss-seidel spectral radius is 0.9876142 estimated iterations to convergence 73 setup time was (sec) 0.3900000 now iterating at: 15:58:29 rms-change max change #iterations 0.1471004 20.80458 at 10iterations 1.4970329E-02 2.673183 at 20iterations 1.5360913E-03 0.2429962 at 30iterations 1.6683647E-04 2.4430275E-02 at 40iterations 2.2239250E-05 3.1509399E-03 at 50iterations finished qdiffx linear iterations at : 15:58:32 total time elapsed so far: 3.380000 # loops : 50 mean,max change (kT/e) : 2.2239250E-05 3.1509399E-03 energy calculations done at 3.380000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.500000 DelPhi exited at 15:58:32 3.508u 0.197s 0:03.99 92.4% 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 Sat Oct 8 2011 at 15:58:32 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: 279 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2339 !!! WARNING: ASL 705 has a net charge of -0.1000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.942242 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): -2.295000 46.29600 ymin,ymax (A): 15.93300 62.52000 zmin,zma (A): -18.56800 36.42000 x,y,z range (A): 48.59100 46.58700 54.98800 scale (grids/A): 1.942242 object centre (A): 22.00050 39.22650 8.926000 number of atom coordinates read : 2339 total number of charged atoms : 2239 net assigned charge : 2.900002 assigned positive charge : 346.3180 centred at (gu) : 90.86118 86.93325 90.75053 assigned negative charge : -343.4188 centred at (gu) : 90.92299 87.37166 90.97814 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 70975 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19866 grid for indexing accessible points = 1.400000 m= 25476 mr = 49663 m= 4485 mr = 18769 m= 294 mr = 3004 m= 4 mr = 122 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 1321 time to turn everything in is 0.3500000 number of dielectric boundary points 29676 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 124 iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 17624 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) : 0.6474140 object centre at (A) : 22.00050 39.22650 8.926000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.4030749E-02 -1.3650333E-02 midg,1,midg; midg,igrid,midg 2.5920033E-02 -8.4759640E-03 1,midg,midg; igrid,midg,midg 5.0028483E-03 -3.8044393E-02 gauss-seidel spectral radius is 0.9986580 estimated iterations to convergence 216 setup time was (sec) 0.5800000 now iterating at: 15:58:33 rms-change max change #iterations 4.149011 214.2874 at 10iterations 1.953016 76.35844 at 20iterations 0.9227480 29.90287 at 30iterations 0.4343168 14.15181 at 40iterations 0.2047053 6.769244 at 50iterations 9.6760899E-02 3.090000 at 60iterations 4.5611937E-02 1.510064 at 70iterations 2.1573877E-02 0.7786512 at 80iterations 1.0143113E-02 0.3015218 at 90iterations 4.7916542E-03 0.1463470 at 100iterations 2.2651346E-03 6.9170952E-02 at 110iterations 1.0748089E-03 3.4870148E-02 at 120iterations finished qdiffx linear iterations at : 15:58:40 total time elapsed so far: 7.980000 # loops : 120 mean,max change (kT/e) : 1.0748089E-03 3.4870148E-02 energy calculations done at 7.980000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.110000 DelPhi exited at 15:58:41 8.112u 0.219s 0:08.68 95.8% 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 Sat Oct 8 2011 at 15:58:41 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: 279 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2339 !!! WARNING: ASL 705 has a net charge of -0.1000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.913363 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): -2.295000 46.29600 ymin,ymax (A): 15.93300 62.52000 zmin,zma (A): -18.56800 36.42000 x,y,z range (A): 48.59100 46.58700 54.98800 scale (grids/A): 2.913363 object centre (A): 22.00050 39.22650 8.926000 number of atom coordinates read : 2339 total number of charged atoms : 2239 net assigned charge : 2.900002 assigned positive charge : 346.3180 centred at (gu) : 91.29179 85.39966 91.12572 assigned negative charge : -343.4188 centred at (gu) : 91.38449 86.05756 91.46710 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 164259 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19866 grid for indexing accessible points = 1.400000 m= 82014 mr = 120208 m= 30582 mr = 67175 m= 8207 mr = 24885 m= 1230 mr = 6366 m= 96 mr = 869 m= 2 mr = 46 m= 0 mr = 0 time to grow re-entrant surface = 0.5300000 no. cavity mid-points inaccessible to solvent = 4258 time to turn everything in is 0.9200000 number of dielectric boundary points 66841 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.020000 number of grid points assigned charge 17907 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) : 1.942242 object centre at (A) : 22.00050 39.22650 8.926000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2196036 -0.2360596 midg,1,midg; midg,igrid,midg 0.1964350 -0.1070874 1,midg,midg; igrid,midg,midg 6.4856537E-02 -0.5618323 gauss-seidel spectral radius is 0.9992581 estimated iterations to convergence 290 setup time was (sec) 1.180000 now iterating at: 15:58:42 rms-change max change #iterations 9.601838 445.3348 at 10iterations 5.603619 128.7444 at 20iterations 3.244632 67.78740 at 30iterations 1.878056 38.73295 at 40iterations 1.085782 22.54900 at 50iterations 0.6263821 11.59085 at 60iterations 0.3614834 6.652356 at 70iterations 0.2080773 3.904356 at 80iterations 0.1198867 2.144197 at 90iterations 6.9010198E-02 1.272896 at 100iterations 3.9582137E-02 0.7439499 at 110iterations 2.2780979E-02 0.4212790 at 120iterations 1.3089860E-02 0.2568054 at 130iterations 7.5432700E-03 0.1461830 at 140iterations 4.3339473E-03 7.9367638E-02 at 150iterations 2.4928891E-03 4.6007156E-02 at 160iterations 1.4407439E-03 2.5115967E-02 at 170iterations 8.3601533E-04 1.7429352E-02 at 180iterations finished qdiffx linear iterations at : 15:58:54 total time elapsed so far: 13.12000 # loops : 180 mean,max change (kT/e) : 8.3601533E-04 1.7429352E-02 energy calculations done at 13.12000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.26000 DelPhi exited at 15:58:55 13.261u 0.239s 0:13.76 98.0% 0+0k 0+0io 0pf+0w