Sun Oct 9 07:58:31 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 07:58:31 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2219 !!! WARNING: NDP 385 has a net charge of -2.8280 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: 0.6990123 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): 4.547000 49.99200 ymin,ymax (A): -24.75400 26.17500 zmin,zma (A): -19.40800 30.26400 x,y,z range (A): 45.44500 50.92900 49.67200 scale (grids/A): 0.6990123 object centre (A): 27.26950 0.7104998 5.428000 number of atom coordinates read : 2219 total number of charged atoms : 2077 net assigned charge : -3.327991 assigned positive charge : 336.8184 centred at (gu) : 89.97091 91.08938 90.14839 assigned negative charge : -340.1467 centred at (gu) : 89.99649 91.18157 90.25834 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 7491 nv = 96 ne = 84 npr = 44933 no. pairs analyzed = 44933 no. exposed pairs = 2927 no. arc points = 20944 no. surface atoms = 966 nbur = 1253 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 534 mr = 4068 m= 6 mr = 90 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 40 time to turn everything in is 0.2700000 number of dielectric boundary points 3873 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1968 ## 166 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 8264 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.5302151E-08 -7.3943418E-08 midg,1,midg; midg,igrid,midg 1.4527120E-08 -7.9164593E-08 1,midg,midg; igrid,midg,midg -1.0997722E-08 -3.3530178E-08 gauss-seidel spectral radius is 0.9893585 estimated iterations to convergence 79 setup time was (sec) 0.5300000 now iterating at: 07:58:32 rms-change max change #iterations 0.1986012 27.81067 at 10iterations 2.3437189E-02 3.013468 at 20iterations 2.8133609E-03 0.4557285 at 30iterations 3.3413540E-04 5.0137520E-02 at 40iterations 4.0284653E-05 5.6257248E-03 at 50iterations finished qdiffx linear iterations at : 07:58:36 total time elapsed so far: 4.040000 # loops : 50 mean,max change (kT/e) : 4.0284653E-05 5.6257248E-03 energy calculations done at 4.040000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.220000 DelPhi exited at 07:58:36 4.221u 0.274s 0:04.76 94.3% 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 07:58:36 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2219 !!! WARNING: NDP 385 has a net charge of -2.8280 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: 2.097037 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): 4.547000 49.99200 ymin,ymax (A): -24.75400 26.17500 zmin,zma (A): -19.40800 30.26400 x,y,z range (A): 45.44500 50.92900 49.67200 scale (grids/A): 2.097037 object centre (A): 27.26950 0.7104998 5.428000 number of atom coordinates read : 2219 total number of charged atoms : 2077 net assigned charge : -3.327991 assigned positive charge : 336.8184 centred at (gu) : 89.91240 93.26796 90.44463 assigned negative charge : -340.1467 centred at (gu) : 89.98957 93.54459 90.77483 start vw surface at 0.1600000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 78953 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20944 grid for indexing accessible points = 1.400000 m= 31157 mr = 53712 m= 6326 mr = 23130 m= 677 mr = 4251 m= 33 mr = 346 m= 0 mr = 9 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 1447 time to turn everything in is 0.6900000 number of dielectric boundary points 35698 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 94 iepsmp to db, and charging done at 0.8300000 number of grid points assigned charge 16492 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) : 0.6990123 object centre at (A) : 27.26950 0.7104998 5.428000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.9768870E-03 -4.3984417E-02 midg,1,midg; midg,igrid,midg 2.9998979E-02 -6.5383031E-03 1,midg,midg; igrid,midg,midg -3.4362189E-03 -3.3520117E-02 gauss-seidel spectral radius is 0.9988346 estimated iterations to convergence 232 setup time was (sec) 1.020000 now iterating at: 07:58:37 rms-change max change #iterations 4.785259 229.7304 at 10iterations 2.361564 76.77720 at 20iterations 1.169139 38.80661 at 30iterations 0.5789937 18.36335 at 40iterations 0.2869466 9.060467 at 50iterations 0.1424058 4.545326 at 60iterations 7.0492454E-02 2.302410 at 70iterations 3.4876995E-02 1.095192 at 80iterations 1.7275659E-02 0.5059090 at 90iterations 8.5858414E-03 0.2918337 at 100iterations 4.2455881E-03 0.1329889 at 110iterations 2.1120291E-03 6.3467026E-02 at 120iterations finished qdiffx linear iterations at : 07:58:46 total time elapsed so far: 9.940000 # loops : 120 mean,max change (kT/e) : 2.1120291E-03 6.3467026E-02 energy calculations done at 9.940000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.12000 DelPhi exited at 07:58:47 10.121u 0.301s 0:10.70 97.3% 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 07:58:47 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2219 !!! WARNING: NDP 385 has a net charge of -2.8280 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: 3.145555 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): 4.547000 49.99200 ymin,ymax (A): -24.75400 26.17500 zmin,zma (A): -19.40800 30.26400 x,y,z range (A): 45.44500 50.92900 49.67200 scale (grids/A): 3.145555 object centre (A): 27.26950 0.7104998 5.428000 number of atom coordinates read : 2219 total number of charged atoms : 2077 net assigned charge : -3.327991 assigned positive charge : 336.8184 centred at (gu) : 89.86836 94.90182 90.66692 assigned negative charge : -340.1467 centred at (gu) : 89.98434 95.31685 91.16228 start vw surface at 0.1300000 fill in re-entrant regions at 0.8400000 boundary points on vw surface= 181723 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20944 grid for indexing accessible points = 1.400000 m= 96401 mr = 129631 m= 40069 mr = 79039 m= 12112 mr = 32756 m= 2673 mr = 9426 m= 400 mr = 1907 m= 29 mr = 252 m= 1 mr = 10 m= 0 mr = 0 time to grow re-entrant surface = 1.010000 no. cavity mid-points inaccessible to solvent = 4900 time to turn everything in is 1.990000 number of dielectric boundary points 80387 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.160000 number of grid points assigned charge 16615 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) : 2.097037 object centre at (A) : 27.26950 0.7104998 5.428000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.1894825E-03 -0.2745456 midg,1,midg; midg,igrid,midg 0.8945371 5.2995555E-02 1,midg,midg; igrid,midg,midg -5.8530316E-02 -0.2865801 gauss-seidel spectral radius is 0.9993040 estimated iterations to convergence 299 setup time was (sec) 2.360000 now iterating at: 07:58:49 rms-change max change #iterations 10.77359 366.4757 at 10iterations 6.339720 135.3325 at 20iterations 3.722219 74.08484 at 30iterations 2.187315 45.69170 at 40iterations 1.285577 24.79280 at 50iterations 0.7539098 13.28599 at 60iterations 0.4423843 7.680679 at 70iterations 0.2593831 4.604770 at 80iterations 0.1515632 2.812560 at 90iterations 8.8668115E-02 1.583279 at 100iterations 5.1813509E-02 0.9113085 at 110iterations 3.0243564E-02 0.5260673 at 120iterations 1.7671913E-02 0.3125591 at 130iterations 1.0331781E-02 0.1757469 at 140iterations 6.0621793E-03 0.1084175 at 150iterations 3.5423487E-03 6.3430846E-02 at 160iterations 2.0756496E-03 3.3985138E-02 at 170iterations 1.2189500E-03 2.3960114E-02 at 180iterations finished qdiffx linear iterations at : 07:59:04 total time elapsed so far: 16.81000 # loops : 180 mean,max change (kT/e) : 1.2189500E-03 2.3960114E-02 energy calculations done at 16.81000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.00000 DelPhi exited at 07:59:04 16.999u 0.330s 0:17.61 98.3% 0+0k 0+0io 0pf+0w