Sat Oct 15 14:20:25 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 14:20:26 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: 330 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4795 !!! WARNING: GLM 169 has a net charge of -0.0940 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: FE 3 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.5102407 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): -16.21300 36.90900 ymin,ymax (A): -30.45900 34.17500 zmin,zma (A): -4.034000 65.73700 x,y,z range (A): 53.12200 64.63400 69.77100 scale (grids/A): 0.5102407 object centre (A): 10.34800 1.858002 30.85150 number of atom coordinates read : 4795 total number of charged atoms : 4544 net assigned charge : 6.706031 assigned positive charge : 721.1574 centred at (gu) : 89.64307 90.45122 88.50834 assigned negative charge : -714.4560 centred at (gu) : 89.53289 90.52709 88.48506 start vw surface at 0.1300000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 7905 nv = 96 ne = 84 npr = 96634 no. pairs analyzed = 96634 no. exposed pairs = 6078 no. arc points = 42499 no. surface atoms = 2029 nbur = 2766 mkacc time = 0.1700000 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 = 1.680000 m= 270 mr = 4049 m= 1 mr = 13 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 4114 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4024 ## 596 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 10486 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.3231346E-11 1.0597234E-10 midg,1,midg; midg,igrid,midg 2.5580957E-10 -1.1185938E-10 1,midg,midg; igrid,midg,midg -2.0756694E-10 3.3972744E-10 gauss-seidel spectral radius is 0.9803607 estimated iterations to convergence 59 setup time was (sec) 0.5200000 now iterating at: 14:20:26 rms-change max change #iterations 6.8904579E-02 10.02739 at 10iterations 3.8622830E-03 0.6077642 at 20iterations 3.5061908E-04 5.0457001E-02 at 30iterations 1.0940582E-04 1.6100168E-02 at 40iterations 4.3638694E-05 6.5054893E-03 at 50iterations finished qdiffx linear iterations at : 14:20:31 total time elapsed so far: 3.530000 # loops : 50 mean,max change (kT/e) : 4.3638694E-05 6.5054893E-03 energy calculations done at 3.530000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.660000 DelPhi exited at 14:20:32 3.665u 0.192s 0:06.00 64.1% 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 14:20:32 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: 330 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4795 !!! WARNING: GLM 169 has a net charge of -0.0940 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: FE 3 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.530722 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): -16.21300 36.90900 ymin,ymax (A): -30.45900 34.17500 zmin,zma (A): -4.034000 65.73700 x,y,z range (A): 53.12200 64.63400 69.77100 scale (grids/A): 1.530722 object centre (A): 10.34800 1.858002 30.85150 number of atom coordinates read : 4795 total number of charged atoms : 4544 net assigned charge : 6.706031 assigned positive charge : 721.1574 centred at (gu) : 88.92799 91.35214 85.52334 assigned negative charge : -714.4560 centred at (gu) : 88.59831 91.58092 85.45494 start vw surface at 0.1200000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 90167 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42499 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 25553 mr = 61872 m= 2170 mr = 16728 m= 45 mr = 880 m= 0 mr = 2 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 221 time to turn everything in is 0.4400000 number of dielectric boundary points 38453 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 559 ## 6 charges are in solution ## iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 34241 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) : 0.5102407 object centre at (A) : 10.34800 1.858002 30.85150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.7820271E-03 2.0389376E-02 midg,1,midg; midg,igrid,midg 1.3422899E-02 -1.4615530E-02 1,midg,midg; igrid,midg,midg -9.5396227E-04 9.6109780E-03 gauss-seidel spectral radius is 0.9981140 estimated iterations to convergence 183 setup time was (sec) 0.6900000 now iterating at: 14:20:33 rms-change max change #iterations 3.816684 172.4292 at 10iterations 1.557597 59.11697 at 20iterations 0.6404787 24.22178 at 30iterations 0.2626011 8.273662 at 40iterations 0.1078553 3.418635 at 50iterations 4.4458598E-02 1.676863 at 60iterations 1.8240608E-02 0.6282921 at 70iterations 7.5179045E-03 0.2670717 at 80iterations 3.1237246E-03 9.7518921E-02 at 90iterations 1.3124237E-03 4.1954041E-02 at 100iterations 5.7288521E-04 1.9555092E-02 at 110iterations 2.7596878E-04 9.9701881E-03 at 120iterations finished qdiffx linear iterations at : 14:20:40 total time elapsed so far: 8.340000 # loops : 120 mean,max change (kT/e) : 2.7596878E-04 9.9701881E-03 energy calculations done at 8.340000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.470000 DelPhi exited at 14:20:41 8.469u 0.237s 0:09.14 95.0% 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 Sat Oct 15 2011 at 14:20:41 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: 330 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4795 !!! WARNING: GLM 169 has a net charge of -0.0940 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: FE 3 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.296083 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): -16.21300 36.90900 ymin,ymax (A): -30.45900 34.17500 zmin,zma (A): -4.034000 65.73700 x,y,z range (A): 53.12200 64.63400 69.77100 scale (grids/A): 2.296083 object centre (A): 10.34800 1.858002 30.85150 number of atom coordinates read : 4795 total number of charged atoms : 4544 net assigned charge : 6.706031 assigned positive charge : 721.1574 centred at (gu) : 88.39175 92.02798 83.28481 assigned negative charge : -714.4560 centred at (gu) : 87.89741 92.37131 83.18230 start vw surface at 0.1300000 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 210185 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42499 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 92794 mr = 152388 m= 22684 mr = 71957 m= 3150 mr = 15854 m= 175 mr = 1848 m= 3 mr = 58 m= 0 mr = 0 time to grow re-entrant surface = 0.6000000 no. cavity mid-points inaccessible to solvent = 867 time to turn everything in is 1.070000 number of dielectric boundary points 86886 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 63 iepsmp to db, and charging done at 1.170000 number of grid points assigned charge 36265 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) : 1.530722 object centre at (A) : 10.34800 1.858002 30.85150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1343343 0.5028166 midg,1,midg; midg,igrid,midg 0.2651860 -0.3013764 1,midg,midg; igrid,midg,midg -8.6817276E-03 0.1398890 gauss-seidel spectral radius is 0.9991654 estimated iterations to convergence 273 setup time was (sec) 1.330000 now iterating at: 14:20:43 rms-change max change #iterations 10.35735 301.6470 at 10iterations 5.930884 160.3004 at 20iterations 3.374111 76.34503 at 30iterations 1.910344 56.66492 at 40iterations 1.078152 21.21912 at 50iterations 0.6055875 12.95273 at 60iterations 0.3397386 6.661179 at 70iterations 0.1903929 4.653157 at 80iterations 0.1063296 1.955498 at 90iterations 5.9250720E-02 1.238972 at 100iterations 3.3102188E-02 0.6807387 at 110iterations 1.8457185E-02 0.3579254 at 120iterations 1.0274829E-02 0.2011337 at 130iterations 5.7205949E-03 0.1103144 at 140iterations 3.1855423E-03 5.9089661E-02 at 150iterations 1.7719843E-03 3.3706665E-02 at 160iterations 9.8825328E-04 1.7787933E-02 at 170iterations 5.5197073E-04 1.0526657E-02 at 180iterations finished qdiffx linear iterations at : 14:20:59 total time elapsed so far: 14.14000 # loops : 180 mean,max change (kT/e) : 5.5197073E-04 1.0526657E-02 energy calculations done at 14.14000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.28000 DelPhi exited at 14:20:59 14.277u 0.267s 0:18.30 79.3% 0+0k 0+0io 0pf+0w