Sat Oct 15 15:28:47 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 Sat Oct 15 2011 at 15:28:47 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: 319 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3834 !!! WARNING: HIR 84 has a net charge of 0.5140 !!! WARNING: SEP 246 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5431218 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): -13.87200 51.27100 ymin,ymax (A): 22.40000 87.94700 zmin,zma (A): 18.39300 77.30000 x,y,z range (A): 65.14300 65.54700 58.90701 scale (grids/A): 0.5431218 object centre (A): 18.69950 55.17350 47.84650 number of atom coordinates read : 3834 total number of charged atoms : 3675 net assigned charge : 9.039027 assigned positive charge : 588.2562 centred at (gu) : 89.42874 90.57810 92.67776 assigned negative charge : -579.2205 centred at (gu) : 89.44586 90.43430 92.80325 start vw surface at 0.1700000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7358 nv = 96 ne = 84 npr = 74571 no. pairs analyzed = 74571 no. exposed pairs = 5187 no. arc points = 37283 no. surface atoms = 1716 nbur = 2118 mkacc time = 0.1600000 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= 303 mr = 3543 m= 0 mr = 14 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3700000 number of dielectric boundary points 4104 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3694 ## 545 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 9607 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.6333778E-10 -9.4955521E-10 midg,1,midg; midg,igrid,midg -5.2092058E-10 1.8567844E-09 1,midg,midg; igrid,midg,midg 7.4977735E-10 3.3928851E-10 gauss-seidel spectral radius is 0.9825969 estimated iterations to convergence 62 setup time was (sec) 0.6000000 now iterating at: 15:28:48 rms-change max change #iterations 8.4889285E-02 13.63129 at 10iterations 5.9201587E-03 1.024929 at 20iterations 5.0771295E-04 9.1983795E-02 at 30iterations 8.3355000E-05 1.6036987E-02 at 40iterations 2.0495729E-05 3.1852722E-03 at 50iterations finished qdiffx linear iterations at : 15:28:51 total time elapsed so far: 3.170000 # loops : 50 mean,max change (kT/e) : 2.0495729E-05 3.1852722E-03 energy calculations done at 3.170000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.360000 DelPhi exited at 15:28:51 3.365u 0.193s 0:03.94 90.1% 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 Sat Oct 15 2011 at 15:28:51 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: 319 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3834 !!! WARNING: HIR 84 has a net charge of 0.5140 !!! WARNING: SEP 246 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.629365 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): -13.87200 51.27100 ymin,ymax (A): 22.40000 87.94700 zmin,zma (A): 18.39300 77.30000 x,y,z range (A): 65.14300 65.54700 58.90701 scale (grids/A): 1.629365 object centre (A): 18.69950 55.17350 47.84650 number of atom coordinates read : 3834 total number of charged atoms : 3675 net assigned charge : 9.039027 assigned positive charge : 588.2562 centred at (gu) : 88.28468 91.73306 98.03212 assigned negative charge : -579.2205 centred at (gu) : 88.33713 91.30235 98.40909 start vw surface at 0.1700000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 79592 reading accessible surface arcs data from file ARCDAT no. of arc points read = 37283 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 24909 mr = 51135 m= 2810 mr = 16622 m= 84 mr = 1350 m= 0 mr = 8 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 134 time to turn everything in is 0.5900000 number of dielectric boundary points 38280 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 470 ## 6 charges are in solution ## iepsmp to db, and charging done at 0.7200000 number of grid points assigned charge 28135 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) : 0.5431218 object centre at (A) : 18.69950 55.17350 47.84650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.2852543E-02 -2.2570575E-03 midg,1,midg; midg,igrid,midg 5.4729660E-03 4.3330304E-02 1,midg,midg; igrid,midg,midg 1.5860945E-02 4.2957142E-03 gauss-seidel spectral radius is 0.9982706 estimated iterations to convergence 191 setup time was (sec) 0.8900000 now iterating at: 15:28:52 rms-change max change #iterations 3.868169 171.5161 at 10iterations 1.634981 53.81118 at 20iterations 0.6954644 23.52182 at 30iterations 0.2940419 9.904602 at 40iterations 0.1250160 4.380489 at 50iterations 5.3207569E-02 1.626259 at 60iterations 2.2718284E-02 0.7530823 at 70iterations 9.6646696E-03 0.3328724 at 80iterations 4.1211555E-03 0.1463823 at 90iterations 1.7645765E-03 5.6566238E-02 at 100iterations 7.6136994E-04 2.3406029E-02 at 110iterations 3.3274281E-04 1.0780334E-02 at 120iterations finished qdiffx linear iterations at : 15:29:00 total time elapsed so far: 7.990000 # loops : 120 mean,max change (kT/e) : 3.3274281E-04 1.0780334E-02 energy calculations done at 7.990000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.160000 DelPhi exited at 15:29:00 8.167u 0.247s 0:08.79 95.5% 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 Sat Oct 15 2011 at 15:29:00 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: 319 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3834 !!! WARNING: HIR 84 has a net charge of 0.5140 !!! WARNING: SEP 246 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.444048 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): -13.87200 51.27100 ymin,ymax (A): 22.40000 87.94700 zmin,zma (A): 18.39300 77.30000 x,y,z range (A): 65.14300 65.54700 58.90701 scale (grids/A): 2.444048 object centre (A): 18.69950 55.17350 47.84650 number of atom coordinates read : 3834 total number of charged atoms : 3675 net assigned charge : 9.039027 assigned positive charge : 588.2562 centred at (gu) : 87.42661 92.59915 102.0480 assigned negative charge : -579.2205 centred at (gu) : 87.50574 91.95341 102.6136 start vw surface at 0.1600000 fill in re-entrant regions at 0.4600000 boundary points on vw surface= 184089 reading accessible surface arcs data from file ARCDAT no. of arc points read = 37283 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 84628 mr = 125878 m= 25567 mr = 65012 m= 4230 mr = 18813 m= 288 mr = 2725 m= 4 mr = 110 m= 0 mr = 0 time to grow re-entrant surface = 0.8200000 no. cavity mid-points inaccessible to solvent = 468 time to turn everything in is 1.420000 number of dielectric boundary points 86268 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 32 iepsmp to db, and charging done at 1.560000 number of grid points assigned charge 29363 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) : 1.629365 object centre at (A) : 18.69950 55.17350 47.84650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1145647 -0.1189473 midg,1,midg; midg,igrid,midg 7.3845671E-03 0.7034840 1,midg,midg; igrid,midg,midg 9.0105608E-02 5.6816217E-02 gauss-seidel spectral radius is 0.9991879 estimated iterations to convergence 277 setup time was (sec) 1.740000 now iterating at: 15:29:02 rms-change max change #iterations 10.10291 305.1805 at 10iterations 5.791999 153.2242 at 20iterations 3.314249 72.91631 at 30iterations 1.880843 41.81874 at 40iterations 1.063653 21.87420 at 50iterations 0.6013507 12.74085 at 60iterations 0.3386351 6.921949 at 70iterations 0.1899735 3.681803 at 80iterations 0.1065995 2.302109 at 90iterations 5.9877615E-02 1.228683 at 100iterations 3.3558510E-02 0.7047262 at 110iterations 1.8827619E-02 0.3763733 at 120iterations 1.0541938E-02 0.1857486 at 130iterations 5.9064762E-03 0.1105194 at 140iterations 3.3129954E-03 6.3995361E-02 at 150iterations 1.8565193E-03 4.1631699E-02 at 160iterations 1.0414656E-03 2.1842957E-02 at 170iterations 5.8790448E-04 1.2016296E-02 at 180iterations finished qdiffx linear iterations at : 15:29:14 total time elapsed so far: 13.63000 # loops : 180 mean,max change (kT/e) : 5.8790448E-04 1.2016296E-02 energy calculations done at 13.63000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.80000 DelPhi exited at 15:29:15 13.806u 0.259s 0:14.41 97.5% 0+0k 0+0io 0pf+0w