Sat Oct 15 13:39:21 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 13:39:24 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3495 !!! WARNING: GLM 242 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5563543 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): -29.69400 30.69000 ymin,ymax (A): -47.06900 6.543000 zmin,zma (A): 66.42200 130.4100 x,y,z range (A): 60.38400 53.61200 63.98801 scale (grids/A): 0.5563543 object centre (A): 0.4980001 -20.26300 98.41600 number of atom coordinates read : 3495 total number of charged atoms : 3337 net assigned charge : 13.90603 assigned positive charge : 521.6408 centred at (gu) : 90.99387 90.55750 91.88014 assigned negative charge : -507.7361 centred at (gu) : 90.96780 90.52250 91.90250 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7505 nv = 96 ne = 84 npr = 63239 no. pairs analyzed = 63239 no. exposed pairs = 5624 no. arc points = 40295 no. surface atoms = 1843 nbur = 1652 mkacc time = 0.1900000 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 = 1.540000 m= 387 mr = 3214 m= 2 mr = 22 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4000000 number of dielectric boundary points 4658 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3934 ## 459 charges are in solution ## iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 9476 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.8260267E-10 1.6114431E-09 midg,1,midg; midg,igrid,midg 7.8661733E-10 1.9053690E-09 1,midg,midg; igrid,midg,midg 7.8974066E-10 1.9909969E-09 gauss-seidel spectral radius is 0.9834065 estimated iterations to convergence 64 setup time was (sec) 0.6700000 now iterating at: 13:39:26 rms-change max change #iterations 8.5316740E-02 13.60731 at 10iterations 6.0280766E-03 0.8784714 at 20iterations 5.8356690E-04 0.1063271 at 30iterations 1.2430588E-04 1.2111664E-02 at 40iterations 3.5637368E-05 3.0860901E-03 at 50iterations finished qdiffx linear iterations at : 13:39:33 total time elapsed so far: 4.090000 # loops : 50 mean,max change (kT/e) : 3.5637368E-05 3.0860901E-03 energy calculations done at 4.090000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.280000 DelPhi exited at 13:39:34 4.279u 0.325s 0:09.69 47.3% 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 Sat Oct 15 2011 at 13:39:34 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 = 3495 !!! WARNING: GLM 242 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.669063 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): -29.69400 30.69000 ymin,ymax (A): -47.06900 6.543000 zmin,zma (A): 66.42200 130.4100 x,y,z range (A): 60.38400 53.61200 63.98801 scale (grids/A): 1.669063 object centre (A): 0.4980001 -20.26300 98.41600 number of atom coordinates read : 3495 total number of charged atoms : 3337 net assigned charge : 13.90603 assigned positive charge : 521.6408 centred at (gu) : 92.98082 91.67188 95.63969 assigned negative charge : -507.7361 centred at (gu) : 92.90274 91.56707 95.70728 start vw surface at 0.1900000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 80566 reading accessible surface arcs data from file ARCDAT no. of arc points read = 40295 grid for indexing accessible points = 1.400000 m= 26625 mr = 49106 m= 3450 mr = 16983 m= 115 mr = 1474 m= 2 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 0.3900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7500000 number of dielectric boundary points 43189 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 392 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.8900000 number of grid points assigned charge 25660 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) : 0.5563543 object centre at (A) : 0.4980001 -20.26300 98.41600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.5686283E-02 5.2573159E-03 midg,1,midg; midg,igrid,midg 9.5214667E-03 2.8967585E-02 1,midg,midg; igrid,midg,midg -3.6478642E-02 1.8432394E-02 gauss-seidel spectral radius is 0.9983665 estimated iterations to convergence 196 setup time was (sec) 1.060000 now iterating at: 13:39:37 rms-change max change #iterations 3.781094 154.8286 at 10iterations 1.637042 60.99915 at 20iterations 0.7120039 23.34233 at 30iterations 0.3080327 10.82698 at 40iterations 0.1339924 4.282896 at 50iterations 5.8309283E-02 2.014465 at 60iterations 2.5392484E-02 0.9030930 at 70iterations 1.1076687E-02 0.4095898 at 80iterations 4.8384322E-03 0.1647701 at 90iterations 2.1166764E-03 7.7278137E-02 at 100iterations 9.2796260E-04 2.9398918E-02 at 110iterations 4.1363432E-04 1.3932228E-02 at 120iterations finished qdiffx linear iterations at : 13:39:59 total time elapsed so far: 9.760000 # loops : 120 mean,max change (kT/e) : 4.1363432E-04 1.3932228E-02 energy calculations done at 9.760000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.950000 DelPhi exited at 13:39:59 9.948u 0.344s 0:25.56 40.2% 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 Sat Oct 15 2011 at 13:40:00 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3495 !!! WARNING: GLM 242 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= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.503594 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): -29.69400 30.69000 ymin,ymax (A): -47.06900 6.543000 zmin,zma (A): 66.42200 130.4100 x,y,z range (A): 60.38400 53.61200 63.98801 scale (grids/A): 2.503594 object centre (A): 0.4980001 -20.26300 98.41600 number of atom coordinates read : 3495 total number of charged atoms : 3337 net assigned charge : 13.90603 assigned positive charge : 521.6408 centred at (gu) : 94.47101 92.50734 98.45930 assigned negative charge : -507.7361 centred at (gu) : 94.35410 92.35062 98.56089 start vw surface at 0.1700000 fill in re-entrant regions at 0.5600000 boundary points on vw surface= 185615 reading accessible surface arcs data from file ARCDAT no. of arc points read = 40295 grid for indexing accessible points = 1.400000 m= 87515 mr = 121313 m= 28684 mr = 65162 m= 5292 mr = 20317 m= 383 mr = 3130 m= 8 mr = 131 m= 0 mr = 0 time to grow re-entrant surface = 1.150000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.840000 number of dielectric boundary points 97444 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 28 iepsmp to db, and charging done at 2.000000 number of grid points assigned charge 26676 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) : 1.669063 object centre at (A) : 0.4980001 -20.26300 98.41600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2093667 0.1089533 midg,1,midg; midg,igrid,midg 2.0181891E-02 0.3728220 1,midg,midg; igrid,midg,midg -0.8310580 0.3086383 gauss-seidel spectral radius is 0.9992397 estimated iterations to convergence 286 setup time was (sec) 2.180000 now iterating at: 13:40:03 rms-change max change #iterations 10.21161 374.4919 at 10iterations 6.141365 169.7931 at 20iterations 3.646272 104.5877 at 30iterations 2.147966 48.04915 at 40iterations 1.257300 27.13016 at 50iterations 0.7313157 16.04253 at 60iterations 0.4234686 9.203278 at 70iterations 0.2443763 4.913918 at 80iterations 0.1410055 2.901623 at 90iterations 8.0980897E-02 1.615140 at 100iterations 4.6452701E-02 1.057975 at 110iterations 2.6644077E-02 0.5187607 at 120iterations 1.5251920E-02 0.2938652 at 130iterations 8.7132491E-03 0.1791668 at 140iterations 4.9825367E-03 0.1024799 at 150iterations 2.8506340E-03 5.4950714E-02 at 160iterations 1.6306739E-03 3.3258438E-02 at 170iterations 9.3009073E-04 1.7784595E-02 at 180iterations finished qdiffx linear iterations at : 13:40:47 total time elapsed so far: 17.17000 # loops : 180 mean,max change (kT/e) : 9.3009073E-04 1.7784595E-02 energy calculations done at 17.17000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.35000 DelPhi exited at 13:40:48 17.348u 0.398s 0:49.31 35.9% 0+0k 0+0io 0pf+0w