Tue Oct 11 08:00:11 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 Tue Oct 11 2011 at 08:00:11 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: 374 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4179 !!! WARNING: HIR 49 has a net charge of 0.5140 !!! WARNING: HIR 97 has a net charge of 0.5140 !!! WARNING: SEP 196 has a net charge of -0.4750 !!! WARNING: GLM 198 has a net charge of -0.0940 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: 0.5238992 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): -11.87300 41.65100 ymin,ymax (A): -36.64900 24.24300 zmin,zma (A): -29.94800 38.00400 x,y,z range (A): 53.52400 60.89200 67.95200 scale (grids/A): 0.5238992 object centre (A): 14.88900 -6.203001 4.028001 number of atom coordinates read : 4179 total number of charged atoms : 4025 net assigned charge : 12.45903 assigned positive charge : 642.5242 centred at (gu) : 91.11666 90.44619 89.52276 assigned negative charge : -630.0687 centred at (gu) : 90.97578 90.44182 89.56257 start vw surface at 0.1300000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 7140 nv = 96 ne = 84 npr = 84800 no. pairs analyzed = 84800 no. exposed pairs = 5149 no. arc points = 35783 no. surface atoms = 1746 nbur = 2433 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.624000 m= 240 mr = 3685 m= 1 mr = 9 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 0.3000000 number of dielectric boundary points 3687 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3640 ## 561 charges are in solution ## iepsmp to db, and charging done at 0.3500000 number of grid points assigned charge 9702 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.2499838E-10 1.3234253E-10 midg,1,midg; midg,igrid,midg 2.5958494E-10 3.6322789E-10 1,midg,midg; igrid,midg,midg -1.9420575E-10 1.1453922E-09 gauss-seidel spectral radius is 0.9813166 estimated iterations to convergence 60 setup time was (sec) 0.4700000 now iterating at: 08:00:12 rms-change max change #iterations 7.6087639E-02 11.78666 at 10iterations 6.4290101E-03 1.236858 at 20iterations 1.1875849E-03 0.2040787 at 30iterations 3.2483431E-04 6.3785553E-02 at 40iterations 9.5325668E-05 1.9676208E-02 at 50iterations finished qdiffx linear iterations at : 08:00:15 total time elapsed so far: 3.380000 # loops : 50 mean,max change (kT/e) : 9.5325668E-05 1.9676208E-02 energy calculations done at 3.380000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.520000 DelPhi exited at 08:00:15 3.524u 0.180s 0:04.04 91.5% 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 Tue Oct 11 2011 at 08:00:15 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: 374 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4179 !!! WARNING: HIR 49 has a net charge of 0.5140 !!! WARNING: HIR 97 has a net charge of 0.5140 !!! WARNING: SEP 196 has a net charge of -0.4750 !!! WARNING: GLM 198 has a net charge of -0.0940 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: 1.571698 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): -11.87300 41.65100 ymin,ymax (A): -36.64900 24.24300 zmin,zma (A): -29.94800 38.00400 x,y,z range (A): 53.52400 60.89200 67.95200 scale (grids/A): 1.571698 object centre (A): 14.88900 -6.203001 4.028001 number of atom coordinates read : 4179 total number of charged atoms : 4025 net assigned charge : 12.45903 assigned positive charge : 642.5242 centred at (gu) : 93.34894 91.33749 88.56715 assigned negative charge : -630.0687 centred at (gu) : 92.92712 91.32523 88.68741 start vw surface at 0.1200000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 80728 reading accessible surface arcs data from file ARCDAT no. of arc points read = 35783 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 23060 mr = 55370 m= 1933 mr = 15234 m= 43 mr = 703 m= 0 mr = 4 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4000000 number of dielectric boundary points 34453 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 514 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 30439 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) : 0.5238992 object centre at (A) : 14.88900 -6.203001 4.028001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.5635617E-02 -9.4068684E-03 midg,1,midg; midg,igrid,midg 1.3426230E-02 1.7460052E-02 1,midg,midg; igrid,midg,midg -2.6429927E-03 1.2557968E-02 gauss-seidel spectral radius is 0.9981470 estimated iterations to convergence 185 setup time was (sec) 0.6200000 now iterating at: 08:00:16 rms-change max change #iterations 3.751992 158.2861 at 10iterations 1.548453 52.14093 at 20iterations 0.6412579 22.63009 at 30iterations 0.2656859 8.820232 at 40iterations 0.1102966 3.659550 at 50iterations 4.5994669E-02 1.457765 at 60iterations 1.9274095E-02 0.6162024 at 70iterations 8.1423288E-03 0.2762184 at 80iterations 3.5362493E-03 0.1194038 at 90iterations 1.6020501E-03 5.5698395E-02 at 100iterations 7.8331260E-04 3.0929565E-02 at 110iterations 4.2099328E-04 1.6616821E-02 at 120iterations finished qdiffx linear iterations at : 08:00:23 total time elapsed so far: 7.780000 # loops : 120 mean,max change (kT/e) : 4.2099328E-04 1.6616821E-02 energy calculations done at 7.780000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.920000 DelPhi exited at 08:00:24 7.918u 0.219s 0:08.56 94.8% 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 Tue Oct 11 2011 at 08:00:24 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: 374 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4179 !!! WARNING: HIR 49 has a net charge of 0.5140 !!! WARNING: HIR 97 has a net charge of 0.5140 !!! WARNING: SEP 196 has a net charge of -0.4750 !!! WARNING: GLM 198 has a net charge of -0.0940 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: 2.357546 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): -11.87300 41.65100 ymin,ymax (A): -36.64900 24.24300 zmin,zma (A): -29.94800 38.00400 x,y,z range (A): 53.52400 60.89200 67.95200 scale (grids/A): 2.357546 object centre (A): 14.88900 -6.203001 4.028001 number of atom coordinates read : 4179 total number of charged atoms : 4025 net assigned charge : 12.45903 assigned positive charge : 642.5242 centred at (gu) : 95.02274 92.00597 87.85032 assigned negative charge : -630.0687 centred at (gu) : 94.39059 91.98756 88.03091 start vw surface at 0.1300000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 188048 reading accessible surface arcs data from file ARCDAT no. of arc points read = 35783 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 83453 mr = 135711 m= 20338 mr = 65274 m= 2579 mr = 14413 m= 136 mr = 1340 m= 1 mr = 47 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 0.9700000 number of dielectric boundary points 77770 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 54 iepsmp to db, and charging done at 1.070000 number of grid points assigned charge 32125 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) : 1.571698 object centre at (A) : 14.88900 -6.203001 4.028001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5894811 -0.1871101 midg,1,midg; midg,igrid,midg 0.2241143 0.2646670 1,midg,midg; igrid,midg,midg -4.1906055E-02 0.1256481 gauss-seidel spectral radius is 0.9991552 estimated iterations to convergence 272 setup time was (sec) 1.210000 now iterating at: 08:00:25 rms-change max change #iterations 9.858232 345.8458 at 10iterations 5.606027 123.8089 at 20iterations 3.164505 69.01496 at 30iterations 1.778889 37.47397 at 40iterations 0.9970584 21.79000 at 50iterations 0.5556766 12.41572 at 60iterations 0.3101525 6.292429 at 70iterations 0.1729950 3.814575 at 80iterations 9.6146517E-02 2.139786 at 90iterations 5.3473201E-02 1.111624 at 100iterations 2.9846143E-02 0.5698165 at 110iterations 1.6621385E-02 0.3406944 at 120iterations 9.2855264E-03 0.1763229 at 130iterations 5.2214419E-03 0.1060371 at 140iterations 2.9584183E-03 5.7311535E-02 at 150iterations 1.7044834E-03 3.7349701E-02 at 160iterations 1.0028862E-03 2.2865295E-02 at 170iterations 6.1458349E-04 1.4362335E-02 at 180iterations finished qdiffx linear iterations at : 08:00:37 total time elapsed so far: 12.76000 # loops : 180 mean,max change (kT/e) : 6.1458349E-04 1.4362335E-02 energy calculations done at 12.76000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.90000 DelPhi exited at 08:00:38 12.898u 0.197s 0:13.64 95.8% 0+0k 0+0io 0pf+0w