Sun Oct 9 15:55:07 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 15:55:07 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5587 !!! WARNING: GLM 113 has a net charge of -0.0940 !!! WARNING: HIR 456 has a net charge of 0.5140 !!! WARNING: HIR 669 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 0.4964509 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): -105.0720 -33.36300 ymin,ymax (A): -57.19800 10.50600 zmin,zma (A): -33.35700 37.23200 x,y,z range (A): 71.70900 67.70400 70.58900 scale (grids/A): 0.4964509 object centre (A): -69.21750 -23.34600 1.937500 number of atom coordinates read : 5587 total number of charged atoms : 5409 net assigned charge : -2.065958 assigned positive charge : 862.6044 centred at (gu) : 89.11314 89.57395 89.18587 assigned negative charge : -864.6780 centred at (gu) : 89.09115 89.64797 89.12855 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 8763 nv = 96 ne = 84 npr = 110304 no. pairs analyzed = 110304 no. exposed pairs = 6864 no. arc points = 47139 no. surface atoms = 2283 nbur = 3304 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 = 1.708000 m= 298 mr = 4674 m= 2 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3800000 number of dielectric boundary points 4383 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4504 ## 707 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 11685 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.3990216E-10 6.4839439E-11 midg,1,midg; midg,igrid,midg 1.2237211E-10 -1.2510289E-10 1,midg,midg; igrid,midg,midg -6.5907023E-11 1.7373551E-11 gauss-seidel spectral radius is 0.9793108 estimated iterations to convergence 58 setup time was (sec) 0.5800000 now iterating at: 15:55:08 rms-change max change #iterations 6.2815964E-02 8.589712 at 10iterations 4.7289571E-03 0.6948547 at 20iterations 1.3682524E-03 0.2292709 at 30iterations 5.2869058E-04 9.0576172E-02 at 40iterations 2.0579349E-04 3.5629272E-02 at 50iterations finished qdiffx linear iterations at : 15:55:11 total time elapsed so far: 3.490000 # loops : 50 mean,max change (kT/e) : 2.0579349E-04 3.5629272E-02 energy calculations done at 3.490000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.620000 DelPhi exited at 15:55:12 3.623u 0.168s 0:04.10 92.1% 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 15:55:12 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5587 !!! WARNING: GLM 113 has a net charge of -0.0940 !!! WARNING: HIR 456 has a net charge of 0.5140 !!! WARNING: HIR 669 has a net charge of 0.5140 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: 1.489353 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): -105.0720 -33.36300 ymin,ymax (A): -57.19800 10.50600 zmin,zma (A): -33.35700 37.23200 x,y,z range (A): 71.70900 67.70400 70.58900 scale (grids/A): 1.489353 object centre (A): -69.21750 -23.34600 1.937500 number of atom coordinates read : 5587 total number of charged atoms : 5409 net assigned charge : -2.065958 assigned positive charge : 862.6044 centred at (gu) : 87.33805 88.71993 87.55597 assigned negative charge : -864.6780 centred at (gu) : 87.27355 88.94382 87.38523 start vw surface at 0.1500000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 99982 reading accessible surface arcs data from file ARCDAT no. of arc points read = 47139 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.624000 m= 30877 mr = 70378 m= 2605 mr = 21082 m= 40 mr = 1031 m= 0 mr = 1 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 1048 time to turn everything in is 0.5000000 number of dielectric boundary points 41012 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 703 ## 20 charges are in solution ## iepsmp to db, and charging done at 0.5900000 number of grid points assigned charge 40244 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) : 0.4964509 object centre at (A) : -69.21750 -23.34600 1.937500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.0669343E-02 5.1273210E-03 midg,1,midg; midg,igrid,midg 1.3640276E-02 -7.9079131E-03 1,midg,midg; igrid,midg,midg -3.6815800E-02 4.6246336E-03 gauss-seidel spectral radius is 0.9980588 estimated iterations to convergence 180 setup time was (sec) 0.7200000 now iterating at: 15:55:13 rms-change max change #iterations 3.966278 146.8661 at 10iterations 1.603430 58.51753 at 20iterations 0.6555470 22.43026 at 30iterations 0.2645870 7.638807 at 40iterations 0.1077686 3.468739 at 50iterations 4.4157334E-02 1.364827 at 60iterations 1.8395605E-02 0.6271896 at 70iterations 7.9988483E-03 0.2727699 at 80iterations 3.8357815E-03 0.1414890 at 90iterations 2.1375625E-03 7.8998566E-02 at 100iterations 1.3628927E-03 5.0975800E-02 at 110iterations 9.3739625E-04 3.4742355E-02 at 120iterations finished qdiffx linear iterations at : 15:55:20 total time elapsed so far: 7.910000 # loops : 120 mean,max change (kT/e) : 9.3739625E-04 3.4742355E-02 energy calculations done at 7.910000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.040000 DelPhi exited at 15:55:20 8.047u 0.188s 0:08.50 96.7% 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 15:55:20 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5587 !!! WARNING: GLM 113 has a net charge of -0.0940 !!! WARNING: HIR 456 has a net charge of 0.5140 !!! WARNING: HIR 669 has a net charge of 0.5140 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: 2.234029 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): -105.0720 -33.36300 ymin,ymax (A): -57.19800 10.50600 zmin,zma (A): -33.35700 37.23200 x,y,z range (A): 71.70900 67.70400 70.58900 scale (grids/A): 2.234029 object centre (A): -69.21750 -23.34600 1.937500 number of atom coordinates read : 5587 total number of charged atoms : 5409 net assigned charge : -2.065958 assigned positive charge : 862.6044 centred at (gu) : 86.00657 88.07956 86.33366 assigned negative charge : -864.6780 centred at (gu) : 85.91013 88.41558 86.07777 start vw surface at 0.1300000 fill in re-entrant regions at 0.3900000 boundary points on vw surface= 233220 reading accessible surface arcs data from file ARCDAT no. of arc points read = 47139 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 109282 mr = 172431 m= 28531 mr = 86670 m= 3579 mr = 20923 m= 126 mr = 2053 m= 2 mr = 17 m= 0 mr = 0 time to grow re-entrant surface = 0.6999999 no. cavity mid-points inaccessible to solvent = 3607 time to turn everything in is 1.200000 number of dielectric boundary points 92646 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 111 iepsmp to db, and charging done at 1.290000 number of grid points assigned charge 43118 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) : 1.489353 object centre at (A) : -69.21750 -23.34600 1.937500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5144662 0.1192255 midg,1,midg; midg,igrid,midg 0.3821526 -0.1355103 1,midg,midg; igrid,midg,midg -0.8979049 0.1779022 gauss-seidel spectral radius is 0.9991584 estimated iterations to convergence 272 setup time was (sec) 1.440000 now iterating at: 15:55:22 rms-change max change #iterations 10.93467 310.7288 at 10iterations 6.251426 136.2841 at 20iterations 3.548887 82.03507 at 30iterations 1.999330 47.55750 at 40iterations 1.121868 29.00049 at 50iterations 0.6273096 13.86435 at 60iterations 0.3509510 6.977174 at 70iterations 0.1957242 3.944221 at 80iterations 0.1093189 2.290159 at 90iterations 6.0658693E-02 1.136795 at 100iterations 3.3696409E-02 0.6107292 at 110iterations 1.8726125E-02 0.3572311 at 120iterations 1.0403701E-02 0.1901436 at 130iterations 5.7933424E-03 0.1114101 at 140iterations 3.2341580E-03 5.6339264E-02 at 150iterations 1.8125037E-03 3.3162117E-02 at 160iterations 1.0300694E-03 1.8861771E-02 at 170iterations 5.9861213E-04 1.2134552E-02 at 180iterations finished qdiffx linear iterations at : 15:55:34 total time elapsed so far: 13.15000 # loops : 180 mean,max change (kT/e) : 5.9861213E-04 1.2134552E-02 energy calculations done at 13.15000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.27000 DelPhi exited at 15:55:34 13.267u 0.234s 0:13.77 97.9% 0+0k 0+0io 0pf+0w