Thu Jan 19 13:58:55 PST 2012 #!/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 Thu Jan 19 2012 at 13:59:01 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: 346 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 6721 !!! WARNING: ARG 48 has a net charge of 0.0400 !!! WARNING: LYS 155 has a net charge of 0.0200 !!! WARNING: LYS 184 has a net charge of 0.0200 !!! WARNING: LYS 217 has a net charge of 0.0200 !!! WARNING: HIZ 357 has a net charge of 0.2000 !!! WARNING: ARG 365 has a net charge of 0.0400 !!! WARNING: HEM 1106 has a net charge of -4.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 0.4330847 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): -5.189000 77.01200 ymin,ymax (A): -0.6610000 75.88600 zmin,zma (A): 167.5770 235.2910 x,y,z range (A): 82.20100 76.54700 67.71400 scale (grids/A): 0.4330847 object centre (A): 35.91150 37.61250 201.4340 number of atom coordinates read : 6721 total number of charged atoms : 6551 net assigned charge : -5.659946 assigned positive charge : 1017.605 centred at (gu) : 88.80226 90.12132 89.40067 assigned negative charge : -1023.275 centred at (gu) : 88.80920 90.19121 89.37280 start vw surface at 0.1600000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7425 nv = 96 ne = 84 npr = 136618 no. pairs analyzed = 136618 no. exposed pairs = 8665 no. arc points = 58560 no. surface atoms = 2926 nbur = 3795 mkacc time = 0.2400000 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 = 1.932000 m= 178 mr = 3527 m= 0 mr = 2 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4300000 number of dielectric boundary points 4074 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4904 ## 1007 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 10290 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.1538049E-12 5.8023112E-13 midg,1,midg; midg,igrid,midg 3.6557307E-12 -6.8932442E-12 1,midg,midg; igrid,midg,midg -1.2033751E-12 -1.3132095E-12 gauss-seidel spectral radius is 0.9729378 estimated iterations to convergence 51 setup time was (sec) 0.6300000 now iterating at: 13:59:06 rms-change max change #iterations 3.2311127E-02 5.251183 at 10iterations 1.7874638E-03 0.3069477 at 20iterations 5.3346588E-04 9.8187447E-02 at 30iterations 1.9550815E-04 3.5496712E-02 at 40iterations 7.1609669E-05 1.2889862E-02 at 50iterations finished qdiffx linear iterations at : 13:59:15 total time elapsed so far: 3.800000 # loops : 50 mean,max change (kT/e) : 7.1609669E-05 1.2889862E-02 energy calculations done at 3.800000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.930000 DelPhi exited at 13:59:18 3.938u 0.177s 0:18.51 22.1% 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 Thu Jan 19 2012 at 13:59:21 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: 346 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 6721 !!! WARNING: ARG 48 has a net charge of 0.0400 !!! WARNING: LYS 155 has a net charge of 0.0200 !!! WARNING: LYS 184 has a net charge of 0.0200 !!! WARNING: LYS 217 has a net charge of 0.0200 !!! WARNING: HIZ 357 has a net charge of 0.2000 !!! WARNING: ARG 365 has a net charge of 0.0400 !!! WARNING: HEM 1106 has a net charge of -4.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.299254 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): -5.189000 77.01200 ymin,ymax (A): -0.6610000 75.88600 zmin,zma (A): 167.5770 235.2910 x,y,z range (A): 82.20100 76.54700 67.71400 scale (grids/A): 1.299254 object centre (A): 35.91150 37.61250 201.4340 number of atom coordinates read : 6721 total number of charged atoms : 6551 net assigned charge : -5.659946 assigned positive charge : 1017.605 centred at (gu) : 86.40478 90.36214 88.20016 assigned negative charge : -1023.275 centred at (gu) : 86.42760 90.57293 88.11823 start vw surface at 0.1600000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 87203 reading accessible surface arcs data from file ARCDAT no. of arc points read = 58560 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.820000 m= 19978 mr = 57708 m= 1054 mr = 11839 m= 6 mr = 286 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 652 time to turn everything in is 0.4600000 number of dielectric boundary points 38408 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1072 ## 31 charges are in solution ## iepsmp to db, and charging done at 0.5600000 number of grid points assigned charge 45569 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) : 0.4330847 object centre at (A) : 35.91150 37.61250 201.4340 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.7101316E-04 -3.7921401E-04 midg,1,midg; midg,igrid,midg -5.3803361E-04 -7.7200057E-03 1,midg,midg; igrid,midg,midg -2.4221367E-03 1.0690257E-03 gauss-seidel spectral radius is 0.9974396 estimated iterations to convergence 158 setup time was (sec) 0.7200000 now iterating at: 13:59:26 rms-change max change #iterations 3.113735 139.5518 at 10iterations 1.104156 46.30730 at 20iterations 0.3906533 12.92175 at 30iterations 0.1384502 4.949194 at 40iterations 4.9264625E-02 1.683636 at 50iterations 1.7526103E-02 0.6577644 at 60iterations 6.3290400E-03 0.2293477 at 70iterations 2.3929123E-03 8.8419914E-02 at 80iterations 1.0138636E-03 3.7646294E-02 at 90iterations 5.2701723E-04 2.0934820E-02 at 100iterations 3.2611613E-04 1.3007164E-02 at 110iterations 2.1861558E-04 8.2063675E-03 at 120iterations finished qdiffx linear iterations at : 13:59:51 total time elapsed so far: 8.820000 # loops : 120 mean,max change (kT/e) : 2.1861558E-04 8.2063675E-03 energy calculations done at 8.820000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.940000 DelPhi exited at 13:59:52 8.947u 0.253s 0:31.33 29.3% 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 Thu Jan 19 2012 at 13:59:54 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: 346 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 6721 !!! WARNING: ARG 48 has a net charge of 0.0400 !!! WARNING: LYS 155 has a net charge of 0.0200 !!! WARNING: LYS 184 has a net charge of 0.0200 !!! WARNING: LYS 217 has a net charge of 0.0200 !!! WARNING: HIZ 357 has a net charge of 0.2000 !!! WARNING: ARG 365 has a net charge of 0.0400 !!! WARNING: HEM 1106 has a net charge of -4.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.948881 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): -5.189000 77.01200 ymin,ymax (A): -0.6610000 75.88600 zmin,zma (A): 167.5770 235.2910 x,y,z range (A): 82.20100 76.54700 67.71400 scale (grids/A): 1.948881 object centre (A): 35.91150 37.61250 201.4340 number of atom coordinates read : 6721 total number of charged atoms : 6551 net assigned charge : -5.659946 assigned positive charge : 1017.605 centred at (gu) : 84.60666 90.54286 87.29955 assigned negative charge : -1023.275 centred at (gu) : 84.64124 90.85950 87.17728 start vw surface at 0.1600000 fill in re-entrant regions at 0.3900000 boundary points on vw surface= 204536 reading accessible surface arcs data from file ARCDAT no. of arc points read = 58560 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.792000 m= 78439 mr = 144141 m= 14009 mr = 57757 m= 1056 mr = 8921 m= 12 mr = 423 m= 0 mr = 0 time to grow re-entrant surface = 0.5799999 no. cavity mid-points inaccessible to solvent = 2186 time to turn everything in is 1.060000 number of dielectric boundary points 86810 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 313 iepsmp to db, and charging done at 1.170000 number of grid points assigned charge 51694 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) : 1.299254 object centre at (A) : 35.91150 37.61250 201.4340 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.0087084E-02 -1.3669008E-02 midg,1,midg; midg,igrid,midg -2.8360257E-02 -0.1500668 1,midg,midg; igrid,midg,midg -4.7355309E-02 0.1210515 gauss-seidel spectral radius is 0.9989876 estimated iterations to convergence 249 setup time was (sec) 1.330000 now iterating at: 14:00:01 rms-change max change #iterations 9.494701 326.8370 at 10iterations 5.151068 121.4605 at 20iterations 2.764042 75.85558 at 30iterations 1.477140 36.89124 at 40iterations 0.7861205 17.26213 at 50iterations 0.4167112 10.45406 at 60iterations 0.2203282 4.830830 at 70iterations 0.1161508 2.891465 at 80iterations 6.1143111E-02 1.306597 at 90iterations 3.2202289E-02 0.7666626 at 100iterations 1.6930168E-02 0.3607407 at 110iterations 8.9149717E-03 0.1837912 at 120iterations 4.6852860E-03 0.1189480 at 130iterations 2.4677832E-03 5.6449890E-02 at 140iterations 1.3095007E-03 2.9596329E-02 at 150iterations 7.0428202E-04 1.5524387E-02 at 160iterations 3.8841576E-04 9.1171265E-03 at 170iterations 2.2337753E-04 5.7249069E-03 at 180iterations finished qdiffx linear iterations at : 14:00:39 total time elapsed so far: 13.91000 # loops : 180 mean,max change (kT/e) : 2.2337753E-04 5.7249069E-03 energy calculations done at 13.91000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.04000 DelPhi exited at 14:00:41 14.046u 0.222s 0:46.92 30.3% 0+0k 0+0io 0pf+0w