Tue Jan 31 22:46:36 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 Tue Jan 31 2012 at 22:46:36 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 ! Automatically converted by prot2crg.py # of charge parameter records: 941 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2300 !!! WARNING: ARG 861 has a net charge of 0.0400 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: 0.6717615 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): -3.320000 49.67500 ymin,ymax (A): 41.90700 88.63400 zmin,zma (A): -4.673000 41.59900 x,y,z range (A): 52.99500 46.72700 46.27200 scale (grids/A): 0.6717615 object centre (A): 23.17750 65.27050 18.46300 number of atom coordinates read : 2300 total number of charged atoms : 2200 net assigned charge : -2.959991 assigned positive charge : 335.6253 centred at (gu) : 90.60403 90.79051 89.98954 assigned negative charge : -338.5859 centred at (gu) : 90.55273 90.88170 89.99472 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 7088 nv = 96 ne = 84 npr = 47239 no. pairs analyzed = 47239 no. exposed pairs = 2913 no. arc points = 20096 no. surface atoms = 990 nbur = 1310 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 436 mr = 3944 m= 4 mr = 68 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2200000 number of dielectric boundary points 3516 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1876 ## 143 charges are in solution ## iepsmp to db, and charging done at 0.2900000 number of grid points assigned charge 8282 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -8.9797316E-09 -1.1340470E-08 midg,1,midg; midg,igrid,midg 9.0724770E-09 -3.7100776E-08 1,midg,midg; igrid,midg,midg -1.9574921E-08 1.9853312E-09 gauss-seidel spectral radius is 0.9884876 estimated iterations to convergence 76 setup time was (sec) 0.4200000 now iterating at: 22:46:37 rms-change max change #iterations 0.1629573 23.70262 at 10iterations 1.7861122E-02 2.382324 at 20iterations 1.9750255E-03 0.2691727 at 30iterations 2.2184025E-04 3.1500101E-02 at 40iterations 2.4130002E-05 2.9163361E-03 at 50iterations finished qdiffx linear iterations at : 22:46:39 total time elapsed so far: 3.350000 # loops : 50 mean,max change (kT/e) : 2.4130002E-05 2.9163361E-03 energy calculations done at 3.350000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.500000 DelPhi exited at 22:46:40 3.504u 0.185s 0:03.99 92.2% 0+0k 0+45688io 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 Jan 31 2012 at 22:46:40 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 ! Automatically converted by prot2crg.py # of charge parameter records: 941 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2300 !!! WARNING: ARG 861 has a net charge of 0.0400 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: 2.015285 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): -3.320000 49.67500 ymin,ymax (A): 41.90700 88.63400 zmin,zma (A): -4.673000 41.59900 x,y,z range (A): 52.99500 46.72700 46.27200 scale (grids/A): 2.015285 object centre (A): 23.17750 65.27050 18.46300 number of atom coordinates read : 2300 total number of charged atoms : 2200 net assigned charge : -2.959991 assigned positive charge : 335.6253 centred at (gu) : 91.81174 92.37096 89.96813 assigned negative charge : -338.5859 centred at (gu) : 91.65816 92.64503 89.98399 start vw surface at 0.1000000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 76022 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20096 grid for indexing accessible points = 1.400000 m= 28457 mr = 53109 m= 5170 mr = 21112 m= 359 mr = 3244 m= 8 mr = 156 m= 0 mr = 2 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 554 time to turn everything in is 0.4800000 number of dielectric boundary points 32393 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 72 iepsmp to db, and charging done at 0.5500000 number of grid points assigned charge 17422 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) : 0.6717615 object centre at (A) : 23.17750 65.27050 18.46300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.7693499E-02 -4.0823504E-02 midg,1,midg; midg,igrid,midg 1.4385993E-02 -2.9402874E-02 1,midg,midg; igrid,midg,midg 5.4293177E-03 4.1204616E-02 gauss-seidel spectral radius is 0.9987488 estimated iterations to convergence 224 setup time was (sec) 0.6800000 now iterating at: 22:46:41 rms-change max change #iterations 4.331386 228.0082 at 10iterations 2.094528 65.46994 at 20iterations 1.014595 31.45752 at 30iterations 0.4899216 17.84556 at 40iterations 0.2365927 7.273535 at 50iterations 0.1147095 3.512318 at 60iterations 5.5512939E-02 1.785926 at 70iterations 2.6780669E-02 0.8841681 at 80iterations 1.2979104E-02 0.4191751 at 90iterations 6.2529109E-03 0.1943238 at 100iterations 3.0364259E-03 9.4463348E-02 at 110iterations 1.4687103E-03 4.3660879E-02 at 120iterations finished qdiffx linear iterations at : 22:46:48 total time elapsed so far: 7.890000 # loops : 120 mean,max change (kT/e) : 1.4687103E-03 4.3660879E-02 energy calculations done at 7.890000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.040000 DelPhi exited at 22:46:49 8.045u 0.216s 0:08.58 96.1% 0+0k 0+45200io 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 Jan 31 2012 at 22:46:49 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 ! Automatically converted by prot2crg.py # of charge parameter records: 941 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2300 !!! WARNING: ARG 861 has a net charge of 0.0400 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: 3.022927 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): -3.320000 49.67500 ymin,ymax (A): 41.90700 88.63400 zmin,zma (A): -4.673000 41.59900 x,y,z range (A): 52.99500 46.72700 46.27200 scale (grids/A): 3.022927 object centre (A): 23.17750 65.27050 18.46300 number of atom coordinates read : 2300 total number of charged atoms : 2200 net assigned charge : -2.959991 assigned positive charge : 335.6253 centred at (gu) : 92.71760 93.55627 89.95206 assigned negative charge : -338.5859 centred at (gu) : 92.48717 93.96754 89.97591 start vw surface at 0.1000000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 175737 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20096 grid for indexing accessible points = 1.400000 m= 89994 mr = 128559 m= 35137 mr = 73944 m= 9395 mr = 28295 m= 1610 mr = 7120 m= 149 mr = 1087 m= 3 mr = 72 m= 0 mr = 0 time to grow re-entrant surface = 0.8500000 no. cavity mid-points inaccessible to solvent = 1738 time to turn everything in is 1.290000 number of dielectric boundary points 72948 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.380000 number of grid points assigned charge 17600 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) : 2.015285 object centre at (A) : 23.17750 65.27050 18.46300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1770105 -0.3425448 midg,1,midg; midg,igrid,midg 0.2346796 -0.2404681 1,midg,midg; igrid,midg,midg 0.1409847 0.3295823 gauss-seidel spectral radius is 0.9992832 estimated iterations to convergence 295 setup time was (sec) 1.510000 now iterating at: 22:46:50 rms-change max change #iterations 10.01191 414.7588 at 10iterations 5.863035 167.2750 at 20iterations 3.440795 73.74412 at 30iterations 2.006278 43.26888 at 40iterations 1.174610 22.52997 at 50iterations 0.6845323 12.41994 at 60iterations 0.3984201 7.306976 at 70iterations 0.2322053 4.497131 at 80iterations 0.1350423 2.569323 at 90iterations 7.8283928E-02 1.317753 at 100iterations 4.5538355E-02 0.7931938 at 110iterations 2.6415862E-02 0.4597707 at 120iterations 1.5367979E-02 0.2730942 at 130iterations 8.9023393E-03 0.1714993 at 140iterations 5.1573655E-03 8.7714672E-02 at 150iterations 2.9926330E-03 5.2648544E-02 at 160iterations 1.7359798E-03 3.2020450E-02 at 170iterations 1.0051649E-03 1.7896175E-02 at 180iterations finished qdiffx linear iterations at : 22:47:02 total time elapsed so far: 12.88000 # loops : 180 mean,max change (kT/e) : 1.0051649E-03 1.7896175E-02 energy calculations done at 12.88000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.03000 DelPhi exited at 22:47:02 13.036u 0.218s 0:13.55 97.7% 0+0k 0+45192io 0pf+0w