Tue Oct 11 08:29:32 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 08:29:32 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: 344 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3173 !!! WARNING: GLM 15 has a net charge of -0.0940 !!! WARNING: ASP 161 has a net charge of -0.2720 !!! WARNING: SEP 220 has a net charge of -0.4750 !!! WARNING: HIR 291 has a net charge of 0.5140 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: 0.5418734 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): -23.18400 41.53600 ymin,ymax (A): -3.834000 42.73500 zmin,zma (A): 32.98900 98.68700 x,y,z range (A): 64.72000 46.56900 65.69801 scale (grids/A): 0.5418734 object centre (A): 9.176002 19.45050 65.83800 number of atom coordinates read : 3173 total number of charged atoms : 3029 net assigned charge : -5.826970 assigned positive charge : 476.6818 centred at (gu) : 89.41051 89.57774 92.64734 assigned negative charge : -482.5099 centred at (gu) : 89.41821 89.62137 92.73089 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 5892 nv = 96 ne = 84 npr = 66361 no. pairs analyzed = 66361 no. exposed pairs = 3695 no. arc points = 26029 no. surface atoms = 1259 nbur = 1914 mkacc time = 0.1100000 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 = 1.596000 m= 228 mr = 3163 m= 1 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2200000 number of dielectric boundary points 2944 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2819 ## 421 charges are in solution ## iepsmp to db, and charging done at 0.2900000 number of grid points assigned charge 7939 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0568920E-10 -1.5803246E-09 midg,1,midg; midg,igrid,midg -2.7740256E-11 -5.0478316E-10 1,midg,midg; igrid,midg,midg -2.8191793E-10 -2.9387093E-10 gauss-seidel spectral radius is 0.9824532 estimated iterations to convergence 62 setup time was (sec) 0.4100000 now iterating at: 08:29:33 rms-change max change #iterations 7.6694287E-02 13.96442 at 10iterations 4.9060867E-03 0.8046522 at 20iterations 3.2730662E-04 4.9385071E-02 at 30iterations 2.5273581E-05 4.0359497E-03 at 40iterations 3.6487111E-06 8.0013275E-04 at 50iterations finished qdiffx linear iterations at : 08:29:36 total time elapsed so far: 3.240000 # loops : 50 mean,max change (kT/e) : 3.6487111E-06 8.0013275E-04 energy calculations done at 3.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.370000 DelPhi exited at 08:29:36 3.378u 0.170s 0:04.02 88.0% 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 08:29:36 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: 344 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3173 !!! WARNING: GLM 15 has a net charge of -0.0940 !!! WARNING: ASP 161 has a net charge of -0.2720 !!! WARNING: SEP 220 has a net charge of -0.4750 !!! WARNING: HIR 291 has a net charge of 0.5140 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: 1.625620 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): -23.18400 41.53600 ymin,ymax (A): -3.834000 42.73500 zmin,zma (A): 32.98900 98.68700 x,y,z range (A): 64.72000 46.56900 65.69801 scale (grids/A): 1.625620 object centre (A): 9.176002 19.45050 65.83800 number of atom coordinates read : 3173 total number of charged atoms : 3029 net assigned charge : -5.826970 assigned positive charge : 476.6818 centred at (gu) : 88.23073 88.73246 97.94112 assigned negative charge : -482.5099 centred at (gu) : 88.25431 88.86354 98.19219 start vw surface at 0.1000000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 65658 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26029 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 21058 mr = 45387 m= 2092 mr = 15095 m= 63 mr = 1071 m= 0 mr = 7 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 1354 time to turn everything in is 0.3300000 number of dielectric boundary points 27311 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 344 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 23129 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) : 0.5418734 object centre at (A) : 9.176002 19.45050 65.83800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.8797828E-02 -1.7904971E-02 midg,1,midg; midg,igrid,midg -2.3347982E-03 -5.5091102E-03 1,midg,midg; igrid,midg,midg -1.7678009E-02 -1.3922463E-02 gauss-seidel spectral radius is 0.9981719 estimated iterations to convergence 186 setup time was (sec) 0.5300000 now iterating at: 08:29:37 rms-change max change #iterations 3.403189 144.7079 at 10iterations 1.411547 50.34067 at 20iterations 0.5865105 23.16416 at 30iterations 0.2447747 8.979704 at 40iterations 0.1016661 3.490601 at 50iterations 4.2168502E-02 1.439880 at 60iterations 1.7638318E-02 0.6227965 at 70iterations 7.3011154E-03 0.2547150 at 80iterations 3.0575092E-03 0.1142752 at 90iterations 1.2701005E-03 4.4774771E-02 at 100iterations 5.2985002E-04 1.9142151E-02 at 110iterations 2.2100152E-04 8.9836121E-03 at 120iterations finished qdiffx linear iterations at : 08:29:44 total time elapsed so far: 7.410000 # loops : 120 mean,max change (kT/e) : 2.2100152E-04 8.9836121E-03 energy calculations done at 7.410000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.540000 DelPhi exited at 08:29:44 7.545u 0.194s 0:08.02 96.3% 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 Tue Oct 11 2011 at 08:29:44 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: 344 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3173 !!! WARNING: GLM 15 has a net charge of -0.0940 !!! WARNING: ASP 161 has a net charge of -0.2720 !!! WARNING: SEP 220 has a net charge of -0.4750 !!! WARNING: HIR 291 has a net charge of 0.5140 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: 2.438430 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): -23.18400 41.53600 ymin,ymax (A): -3.834000 42.73500 zmin,zma (A): 32.98900 98.68700 x,y,z range (A): 64.72000 46.56900 65.69801 scale (grids/A): 2.438430 object centre (A): 9.176002 19.45050 65.83800 number of atom coordinates read : 3173 total number of charged atoms : 3029 net assigned charge : -5.826970 assigned positive charge : 476.6818 centred at (gu) : 87.34610 88.09850 101.9114 assigned negative charge : -482.5099 centred at (gu) : 87.38141 88.29533 102.2882 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 152566 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26029 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 72852 mr = 110822 m= 21204 mr = 58998 m= 3342 mr = 16347 m= 272 mr = 2162 m= 5 mr = 153 m= 0 mr = 0 time to grow re-entrant surface = 0.4400000 no. cavity mid-points inaccessible to solvent = 4577 time to turn everything in is 0.8000000 number of dielectric boundary points 61759 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 27 iepsmp to db, and charging done at 0.8800000 number of grid points assigned charge 24198 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) : 1.625620 object centre at (A) : 9.176002 19.45050 65.83800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2005313 -8.5977018E-02 midg,1,midg; midg,igrid,midg -3.0210074E-02 -7.3770955E-02 1,midg,midg; igrid,midg,midg -0.3364570 -0.2791067 gauss-seidel spectral radius is 0.9991328 estimated iterations to convergence 268 setup time was (sec) 1.020000 now iterating at: 08:29:46 rms-change max change #iterations 8.747125 281.4933 at 10iterations 4.849496 116.9381 at 20iterations 2.687909 63.66279 at 30iterations 1.479481 33.37380 at 40iterations 0.8185639 16.32629 at 50iterations 0.4505090 9.741489 at 60iterations 0.2473411 5.318953 at 70iterations 0.1357053 2.728130 at 80iterations 7.4524231E-02 1.470651 at 90iterations 4.0891200E-02 0.8611488 at 100iterations 2.2454727E-02 0.4811611 at 110iterations 1.2284124E-02 0.2534113 at 120iterations 6.7456039E-03 0.1360321 at 130iterations 3.6991274E-03 7.9959869E-02 at 140iterations 2.0314544E-03 4.1569471E-02 at 150iterations 1.1135911E-03 2.1781921E-02 at 160iterations 6.1010371E-04 1.2791157E-02 at 170iterations 3.3436675E-04 7.3204041E-03 at 180iterations finished qdiffx linear iterations at : 08:29:56 total time elapsed so far: 11.84000 # loops : 180 mean,max change (kT/e) : 3.3436675E-04 7.3204041E-03 energy calculations done at 11.84000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.97000 DelPhi exited at 08:29:57 11.976u 0.207s 0:12.67 96.0% 0+0k 0+0io 0pf+0w