Sun Oct 9 14:19:19 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 14:19:19 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2783 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: 0.6134124 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): -30.67000 17.82900 ymin,ymax (A): -31.40500 22.73900 zmin,zma (A): -13.48100 44.55500 x,y,z range (A): 48.49900 54.14400 58.03600 scale (grids/A): 0.6134124 object centre (A): -6.420500 -4.333000 15.53700 number of atom coordinates read : 2783 total number of charged atoms : 2642 net assigned charge : 3.000008 assigned positive charge : 422.0413 centred at (gu) : 90.67325 89.79237 89.25629 assigned negative charge : -419.0423 centred at (gu) : 90.79781 89.86936 89.20171 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6882 nv = 96 ne = 84 npr = 56026 no. pairs analyzed = 56026 no. exposed pairs = 3517 no. arc points = 24464 no. surface atoms = 1190 nbur = 1593 mkacc time = 8.9999996E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 386 mr = 3641 m= 2 mr = 45 m= 0 mr = 0 time to grow re-entrant surface = 9.9999987E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2100000 number of dielectric boundary points 3584 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2457 ## 231 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 8546 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.4390220E-09 4.4576338E-09 midg,1,midg; midg,igrid,midg 6.8724111E-09 -2.4211249E-09 1,midg,midg; igrid,midg,midg 8.0100655E-09 -6.3364425E-09 gauss-seidel spectral radius is 0.9862566 estimated iterations to convergence 70 setup time was (sec) 0.3900000 now iterating at: 14:19:20 rms-change max change #iterations 0.1225084 21.07555 at 10iterations 1.0885154E-02 1.736317 at 20iterations 1.0058588E-03 0.1641750 at 30iterations 9.0468173E-05 1.3641357E-02 at 40iterations 9.0517251E-06 1.4572144E-03 at 50iterations finished qdiffx linear iterations at : 14:19:23 total time elapsed so far: 3.210000 # loops : 50 mean,max change (kT/e) : 9.0517251E-06 1.4572144E-03 energy calculations done at 3.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.350000 DelPhi exited at 14:19:23 3.350u 0.162s 0:03.79 92.6% 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 14:19:23 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2783 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: 1.840237 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): -30.67000 17.82900 ymin,ymax (A): -31.40500 22.73900 zmin,zma (A): -13.48100 44.55500 x,y,z range (A): 48.49900 54.14400 58.03600 scale (grids/A): 1.840237 object centre (A): -6.420500 -4.333000 15.53700 number of atom coordinates read : 2783 total number of charged atoms : 2642 net assigned charge : 3.000008 assigned positive charge : 422.0413 centred at (gu) : 92.01923 89.37644 87.76800 assigned negative charge : -419.0423 centred at (gu) : 92.39340 89.60778 87.60467 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 74413 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24464 grid for indexing accessible points = 1.400000 m= 25697 mr = 50493 m= 3705 mr = 18242 m= 206 mr = 2096 m= 2 mr = 75 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 33117 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 186 iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 20636 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) : 0.6134124 object centre at (A) : -6.420500 -4.333000 15.53700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.6688221E-02 -4.0159980E-03 midg,1,midg; midg,igrid,midg 8.2772514E-03 1.3501528E-02 1,midg,midg; igrid,midg,midg 1.5337647E-02 9.6522653E-03 gauss-seidel spectral radius is 0.9985639 estimated iterations to convergence 209 setup time was (sec) 0.5800000 now iterating at: 14:19:24 rms-change max change #iterations 4.122136 169.7276 at 10iterations 1.883924 68.89305 at 20iterations 0.8624380 28.77274 at 30iterations 0.3957337 13.05893 at 40iterations 0.1818440 6.189740 at 50iterations 8.3313696E-02 2.900530 at 60iterations 3.8291860E-02 1.273611 at 70iterations 1.7659383E-02 0.5268593 at 80iterations 8.0980500E-03 0.2435760 at 90iterations 3.7172374E-03 0.1194344 at 100iterations 1.7171246E-03 5.2204132E-02 at 110iterations 7.8755873E-04 2.6760101E-02 at 120iterations finished qdiffx linear iterations at : 14:19:31 total time elapsed so far: 7.540000 # loops : 120 mean,max change (kT/e) : 7.8755873E-04 2.6760101E-02 energy calculations done at 7.540000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.680000 DelPhi exited at 14:19:31 7.680u 0.201s 0:08.27 95.2% 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 14:19:31 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2783 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: 2.760356 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): -30.67000 17.82900 ymin,ymax (A): -31.40500 22.73900 zmin,zma (A): -13.48100 44.55500 x,y,z range (A): 48.49900 54.14400 58.03600 scale (grids/A): 2.760356 object centre (A): -6.420500 -4.333000 15.53700 number of atom coordinates read : 2783 total number of charged atoms : 2642 net assigned charge : 3.000008 assigned positive charge : 422.0413 centred at (gu) : 93.02876 89.06456 86.65176 assigned negative charge : -419.0423 centred at (gu) : 93.58993 89.41175 86.40691 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 172342 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24464 grid for indexing accessible points = 1.400000 m= 84521 mr = 123266 m= 28939 mr = 67625 m= 6366 mr = 22399 m= 847 mr = 4496 m= 54 mr = 566 m= 1 mr = 21 m= 0 mr = 0 time to grow re-entrant surface = 0.5300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.9400000 number of dielectric boundary points 74697 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.030000 number of grid points assigned charge 21129 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) : 1.840237 object centre at (A) : -6.420500 -4.333000 15.53700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.7017106 5.7131592E-03 midg,1,midg; midg,igrid,midg 7.4320696E-02 0.1760443 1,midg,midg; igrid,midg,midg 0.1088190 0.1070454 gauss-seidel spectral radius is 0.9992433 estimated iterations to convergence 287 setup time was (sec) 1.170000 now iterating at: 14:19:33 rms-change max change #iterations 9.966792 316.2142 at 10iterations 5.911535 161.8792 at 20iterations 3.452986 70.95486 at 30iterations 2.009008 44.73015 at 40iterations 1.163944 24.35760 at 50iterations 0.6737657 15.67455 at 60iterations 0.3875991 8.263996 at 70iterations 0.2232573 4.321186 at 80iterations 0.1280470 2.551003 at 90iterations 7.3610246E-02 1.385036 at 100iterations 4.2187363E-02 0.8098221 at 110iterations 2.4193924E-02 0.4698143 at 120iterations 1.3826285E-02 0.2523470 at 130iterations 7.9202084E-03 0.1559885 at 140iterations 4.5303325E-03 8.1805229E-02 at 150iterations 2.5991995E-03 5.0163269E-02 at 160iterations 1.4905585E-03 2.8331757E-02 at 170iterations 8.5659267E-04 1.5751839E-02 at 180iterations finished qdiffx linear iterations at : 14:19:44 total time elapsed so far: 12.56000 # loops : 180 mean,max change (kT/e) : 8.5659267E-04 1.5751839E-02 energy calculations done at 12.56000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.70000 DelPhi exited at 14:19:44 12.700u 0.216s 0:13.18 97.9% 0+0k 0+0io 0pf+0w