Sun Oct 9 03:57:13 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 Sun Oct 9 2011 at 03:57:13 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: 355 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4627 !!! WARNING: HIR 58 has a net charge of 0.5140 !!! WARNING: GLM 161 has a net charge of -0.0940 !!! WARNING: HIZ 357 has a net charge of 0.2000 !!! WARNING: HEM 2209 has a net charge of 1.4000 !!! WARNING: FE 5 has a net charge of 1.4000 !!! WARNING: FE 6 has a net charge of 1.4000 !!! WARNING: FE 7 has a net charge of 1.4000 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: 0.3075727 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): 3.763000 84.72600 ymin,ymax (A): -56.14600 11.93500 zmin,zma (A): -42.01500 73.73000 x,y,z range (A): 80.96300 68.08100 115.7450 scale (grids/A): 0.3075727 object centre (A): 44.24450 -22.10550 15.85750 number of atom coordinates read : 4627 total number of charged atoms : 4306 net assigned charge : 21.72001 assigned positive charge : 675.2064 centred at (gu) : 87.05395 88.86690 82.01310 assigned negative charge : -653.4908 centred at (gu) : 86.94051 88.85322 81.94878 start vw surface at 0.2100000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 2266 nv = 96 ne = 84 npr = 93066 no. pairs analyzed = 93066 no. exposed pairs = 6011 no. arc points = 42335 no. surface atoms = 2010 nbur = 2617 mkacc time = 0.2600000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 2.766400 m= 33 mr = 895 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5000000 number of dielectric boundary points 1404 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1977 ## 674 charges are in solution ## iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 3140 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.8654143E-16 6.8113642E-18 midg,1,midg; midg,igrid,midg 1.3594835E-16 7.1833986E-17 1,midg,midg; igrid,midg,midg -1.1549662E-16 6.5520176E-17 gauss-seidel spectral radius is 0.9470770 estimated iterations to convergence 37 setup time was (sec) 0.8000000 now iterating at: 03:57:14 rms-change max change #iterations 5.9237513E-03 2.192966 at 10iterations 6.1491621E-04 0.2079678 at 20iterations 8.7114269E-05 3.4175873E-02 at 30iterations 1.3006140E-05 5.3691864E-03 at 40iterations 1.9705406E-06 8.3541870E-04 at 50iterations finished qdiffx linear iterations at : 03:57:18 total time elapsed so far: 4.540000 # loops : 50 mean,max change (kT/e) : 1.9705406E-06 8.3541870E-04 energy calculations done at 4.540000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.710000 DelPhi exited at 03:57:18 4.716u 0.265s 0:05.28 94.1% 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 Sun Oct 9 2011 at 03:57:18 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: 355 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4627 !!! WARNING: HIR 58 has a net charge of 0.5140 !!! WARNING: GLM 161 has a net charge of -0.0940 !!! WARNING: HIZ 357 has a net charge of 0.2000 !!! WARNING: HEM 2209 has a net charge of 1.4000 !!! WARNING: FE 5 has a net charge of 1.4000 !!! WARNING: FE 6 has a net charge of 1.4000 !!! WARNING: FE 7 has a net charge of 1.4000 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: 0.9227180 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): 3.763000 84.72600 ymin,ymax (A): -56.14600 11.93500 zmin,zma (A): -42.01500 73.73000 x,y,z range (A): 80.96300 68.08100 115.7450 scale (grids/A): 0.9227180 object centre (A): 44.24450 -22.10550 15.85750 number of atom coordinates read : 4627 total number of charged atoms : 4306 net assigned charge : 21.72001 assigned positive charge : 675.2064 centred at (gu) : 81.16034 86.59903 66.03759 assigned negative charge : -653.4908 centred at (gu) : 80.82104 86.55939 65.84635 start vw surface at 0.2100000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 28968 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42335 initial cube size too small, in assigning accessible points to a grid therefore rescaling... initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 2.591680 m= 3476 mr = 17337 m= 49 mr = 1312 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 317 time to turn everything in is 0.4000000 number of dielectric boundary points 13844 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1672 ## 142 charges are in solution ## iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 23454 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) : 0.3075727 object centre at (A) : 44.24450 -22.10550 15.85750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.8382048E-03 3.6630529E-04 midg,1,midg; midg,igrid,midg 8.1574406E-05 5.6428784E-05 1,midg,midg; igrid,midg,midg -1.1221646E-04 8.1393133E-05 gauss-seidel spectral radius is 0.9940647 estimated iterations to convergence 105 setup time was (sec) 0.7200000 now iterating at: 03:57:19 rms-change max change #iterations 0.8459926 86.29124 at 10iterations 0.1760238 11.10085 at 20iterations 3.6920611E-02 2.842026 at 30iterations 8.7403441E-03 0.6057968 at 40iterations 2.7556422E-03 0.1648140 at 50iterations 1.2133972E-03 6.8331718E-02 at 60iterations 5.9595029E-04 2.9643059E-02 at 70iterations 3.0269442E-04 1.5086174E-02 at 80iterations 1.5478858E-04 7.7457428E-03 at 90iterations 7.9276600E-05 3.9873123E-03 at 100iterations 4.0671312E-05 2.0523071E-03 at 110iterations 2.0874319E-05 1.0557175E-03 at 120iterations finished qdiffx linear iterations at : 03:57:28 total time elapsed so far: 9.150000 # loops : 120 mean,max change (kT/e) : 2.0874319E-05 1.0557175E-03 energy calculations done at 9.150000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.330000 DelPhi exited at 03:57:28 9.331u 0.339s 0:09.95 97.0% 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 Sun Oct 9 2011 at 03:57:28 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: 355 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4627 !!! WARNING: HIR 58 has a net charge of 0.5140 !!! WARNING: GLM 161 has a net charge of -0.0940 !!! WARNING: HIZ 357 has a net charge of 0.2000 !!! WARNING: HEM 2209 has a net charge of 1.4000 !!! WARNING: FE 5 has a net charge of 1.4000 !!! WARNING: FE 6 has a net charge of 1.4000 !!! WARNING: FE 7 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 1.384077 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): 3.763000 84.72600 ymin,ymax (A): -56.14600 11.93500 zmin,zma (A): -42.01500 73.73000 x,y,z range (A): 80.96300 68.08100 115.7450 scale (grids/A): 1.384077 object centre (A): 44.24450 -22.10550 15.85750 number of atom coordinates read : 4627 total number of charged atoms : 4306 net assigned charge : 21.72001 assigned positive charge : 675.2064 centred at (gu) : 76.74017 84.89818 54.05598 assigned negative charge : -653.4908 centred at (gu) : 76.23138 84.83904 53.76939 start vw surface at 0.2400000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 69364 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42335 initial cube size too small, in assigning accessible points to a grid therefore rescaling... initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 2.562560 m= 16763 mr = 45105 m= 1010 mr = 10327 m= 7 mr = 281 m= 0 mr = 0 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 1106 time to turn everything in is 0.7700000 number of dielectric boundary points 31431 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 688 ## 18 charges are in solution ## iepsmp to db, and charging done at 0.9100000 number of grid points assigned charge 31060 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) : 0.9227180 object centre at (A) : 44.24450 -22.10550 15.85750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2620478 1.0945939E-02 midg,1,midg; midg,igrid,midg 4.7380091E-03 3.1467041E-03 1,midg,midg; igrid,midg,midg -7.8162905E-03 9.0615638E-03 gauss-seidel spectral radius is 0.9974021 estimated iterations to convergence 156 setup time was (sec) 1.120000 now iterating at: 03:57:30 rms-change max change #iterations 3.295554 147.9251 at 10iterations 1.215694 56.64115 at 20iterations 0.4423184 19.14918 at 30iterations 0.1590804 6.910439 at 40iterations 5.7510499E-02 2.472984 at 50iterations 2.0504270E-02 0.8213286 at 60iterations 7.3499377E-03 0.3015709 at 70iterations 2.6307974E-03 0.1079159 at 80iterations 9.4733137E-04 3.9630890E-02 at 90iterations 3.4451124E-04 1.3931274E-02 at 100iterations 1.2712025E-04 5.2986145E-03 at 110iterations 4.8566009E-05 2.3841858E-03 at 120iterations 1.9434880E-05 1.1215210E-03 at 130iterations 8.3107043E-06 5.1498413E-04 at 140iterations 3.7978712E-06 2.5558472E-04 at 150iterations 1.9267886E-06 1.6403198E-04 at 160iterations 1.1593629E-06 9.5367432E-05 at 170iterations 8.8280433E-07 6.1035156E-05 at 180iterations finished qdiffx linear iterations at : 03:57:43 total time elapsed so far: 14.31000 # loops : 180 mean,max change (kT/e) : 8.8280433E-07 6.1035156E-05 energy calculations done at 14.31000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.49000 DelPhi exited at 03:57:43 14.495u 0.313s 0:15.12 97.8% 0+0k 0+0io 0pf+0w