Mon Oct 10 12:11:48 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 Mon Oct 10 2011 at 12:11:48 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2117 !!! WARNING: SEP 37 has a net charge of -0.4750 !!! WARNING: LYS 209 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.7353548 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): 40.86300 89.27500 ymin,ymax (A): -9.336000 35.47500 zmin,zma (A): 21.44600 68.60000 x,y,z range (A): 48.41200 44.81100 47.15400 scale (grids/A): 0.7353548 object centre (A): 65.06900 13.06950 45.02300 number of atom coordinates read : 2117 total number of charged atoms : 1976 net assigned charge : -6.746984 assigned positive charge : 317.0199 centred at (gu) : 89.45726 90.76437 90.17857 assigned negative charge : -323.7670 centred at (gu) : 89.47726 90.85023 90.34111 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 7877 nv = 96 ne = 84 npr = 43580 no. pairs analyzed = 43580 no. exposed pairs = 2689 no. arc points = 18774 no. surface atoms = 910 nbur = 1207 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 563 mr = 4402 m= 3 mr = 114 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 17 time to turn everything in is 0.2600000 number of dielectric boundary points 3927 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1579 ## 128 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 8369 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.1366530E-08 -2.6943553E-07 midg,1,midg; midg,igrid,midg -2.4026944E-08 -2.1597928E-07 1,midg,midg; igrid,midg,midg -9.6677716E-08 -1.1328482E-07 gauss-seidel spectral radius is 0.9903649 estimated iterations to convergence 83 setup time was (sec) 0.5300000 now iterating at: 12:11:49 rms-change max change #iterations 0.2384826 41.90668 at 10iterations 3.1662717E-02 4.665985 at 20iterations 4.1619171E-03 0.5042953 at 30iterations 5.6553510E-04 8.1207275E-02 at 40iterations 7.5810727E-05 9.7703934E-03 at 50iterations finished qdiffx linear iterations at : 12:11:53 total time elapsed so far: 4.240000 # loops : 50 mean,max change (kT/e) : 7.5810727E-05 9.7703934E-03 energy calculations done at 4.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.410000 DelPhi exited at 12:11:53 4.418u 0.388s 0:05.16 92.8% 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 Mon Oct 10 2011 at 12:11:53 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2117 !!! WARNING: SEP 37 has a net charge of -0.4750 !!! WARNING: LYS 209 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.206064 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): 40.86300 89.27500 ymin,ymax (A): -9.336000 35.47500 zmin,zma (A): 21.44600 68.60000 x,y,z range (A): 48.41200 44.81100 47.15400 scale (grids/A): 2.206064 object centre (A): 65.06900 13.06950 45.02300 number of atom coordinates read : 2117 total number of charged atoms : 1976 net assigned charge : -6.746984 assigned positive charge : 317.0199 centred at (gu) : 88.37174 92.29320 90.53589 assigned negative charge : -323.7670 centred at (gu) : 88.43175 92.55054 91.02354 start vw surface at 0.1000000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 82866 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18774 grid for indexing accessible points = 1.400000 m= 33783 mr = 57407 m= 7409 mr = 25836 m= 764 mr = 5187 m= 20 mr = 428 m= 0 mr = 2 time to grow re-entrant surface = 0.3800000 no. cavity mid-points inaccessible to solvent = 352 time to turn everything in is 0.6800000 number of dielectric boundary points 35982 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 53 iepsmp to db, and charging done at 0.8400000 number of grid points assigned charge 15741 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) : 0.7353548 object centre at (A) : 65.06900 13.06950 45.02300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.8824183E-03 -0.1274036 midg,1,midg; midg,igrid,midg -2.8632669E-02 -4.6529412E-02 1,midg,midg; igrid,midg,midg 1.6555447E-03 -5.0536799E-03 gauss-seidel spectral radius is 0.9989160 estimated iterations to convergence 240 setup time was (sec) 1.020000 now iterating at: 12:11:55 rms-change max change #iterations 5.031853 195.3387 at 10iterations 2.544910 84.40364 at 20iterations 1.290040 36.39886 at 30iterations 0.6567835 19.55426 at 40iterations 0.3328595 10.08630 at 50iterations 0.1690761 5.200125 at 60iterations 8.6096644E-02 2.492870 at 70iterations 4.3760408E-02 1.322937 at 80iterations 2.2235570E-02 0.6110778 at 90iterations 1.1278840E-02 0.3307292 at 100iterations 5.7516973E-03 0.1806450 at 110iterations 2.9244872E-03 8.4792137E-02 at 120iterations finished qdiffx linear iterations at : 12:12:04 total time elapsed so far: 10.54000 # loops : 120 mean,max change (kT/e) : 2.9244872E-03 8.4792137E-02 energy calculations done at 10.54000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.70000 DelPhi exited at 12:12:05 10.705u 0.442s 0:11.47 97.1% 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 12:12:05 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2117 !!! WARNING: SEP 37 has a net charge of -0.4750 !!! WARNING: LYS 209 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 3.309097 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): 40.86300 89.27500 ymin,ymax (A): -9.336000 35.47500 zmin,zma (A): 21.44600 68.60000 x,y,z range (A): 48.41200 44.81100 47.15400 scale (grids/A): 3.309097 object centre (A): 65.06900 13.06950 45.02300 number of atom coordinates read : 2117 total number of charged atoms : 1976 net assigned charge : -6.746984 assigned positive charge : 317.0199 centred at (gu) : 87.55743 93.43980 90.80382 assigned negative charge : -323.7670 centred at (gu) : 87.64764 93.82579 91.53528 start vw surface at 0.1200000 fill in re-entrant regions at 0.8800000 boundary points on vw surface= 190999 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18774 grid for indexing accessible points = 1.400000 m= 102707 mr = 138318 m= 44349 mr = 85485 m= 14236 mr = 36912 m= 3111 mr = 11327 m= 396 mr = 2397 m= 24 mr = 237 m= 0 mr = 8 time to grow re-entrant surface = 1.180000 no. cavity mid-points inaccessible to solvent = 1175 time to turn everything in is 2.190000 number of dielectric boundary points 81138 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.330000 number of grid points assigned charge 15808 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) : 2.206064 object centre at (A) : 65.06900 13.06950 45.02300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.6507676E-02 -1.222108 midg,1,midg; midg,igrid,midg -0.2679287 -0.2533866 1,midg,midg; igrid,midg,midg -0.1022025 -4.0094454E-02 gauss-seidel spectral radius is 0.9993162 estimated iterations to convergence 302 setup time was (sec) 2.520000 now iterating at: 12:12:08 rms-change max change #iterations 10.90584 432.8497 at 10iterations 6.414495 117.9789 at 20iterations 3.778763 68.39955 at 30iterations 2.217630 38.43316 at 40iterations 1.305476 23.25116 at 50iterations 0.7662137 12.60302 at 60iterations 0.4493494 6.848761 at 70iterations 0.2639823 4.687603 at 80iterations 0.1549250 2.589406 at 90iterations 9.0895429E-02 1.372044 at 100iterations 5.3244945E-02 0.9681139 at 110iterations 3.1252597E-02 0.5275722 at 120iterations 1.8345125E-02 0.2866974 at 130iterations 1.0776742E-02 0.1765685 at 140iterations 6.3157668E-03 0.1083546 at 150iterations 3.7062182E-03 5.7358265E-02 at 160iterations 2.1789845E-03 3.5775661E-02 at 170iterations 1.2804649E-03 1.9746065E-02 at 180iterations finished qdiffx linear iterations at : 12:12:24 total time elapsed so far: 18.94000 # loops : 180 mean,max change (kT/e) : 1.2804649E-03 1.9746065E-02 energy calculations done at 18.94000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.12000 DelPhi exited at 12:12:25 19.120u 0.483s 0:20.12 97.4% 0+0k 0+0io 0pf+0w