Tue Oct 11 03:16:05 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 Tue Oct 11 2011 at 03:16:05 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: 281 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2704 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5929973 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): -28.59800 26.83100 ymin,ymax (A): -21.78900 38.24500 zmin,zma (A): -32.89200 24.61500 x,y,z range (A): 55.42900 60.03400 57.50700 scale (grids/A): 0.5929973 object centre (A): -0.8835001 8.228002 -4.138499 number of atom coordinates read : 2704 total number of charged atoms : 2554 net assigned charge : -4.499988 assigned positive charge : 396.5138 centred at (gu) : 89.19875 88.49538 92.90937 assigned negative charge : -401.0146 centred at (gu) : 89.19341 88.58938 92.94502 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6531 nv = 96 ne = 84 npr = 52210 no. pairs analyzed = 52210 no. exposed pairs = 4037 no. arc points = 28985 no. surface atoms = 1325 nbur = 1379 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 324 mr = 3039 m= 0 mr = 16 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 3800 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2838 ## 308 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 8083 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.6199345E-10 -5.0682187E-09 midg,1,midg; midg,igrid,midg 1.8279760E-09 -3.0939977E-09 1,midg,midg; igrid,midg,midg -2.0094555E-09 -1.1413683E-09 gauss-seidel spectral radius is 0.9853130 estimated iterations to convergence 68 setup time was (sec) 0.5400000 now iterating at: 03:16:05 rms-change max change #iterations 0.1002147 19.21709 at 10iterations 8.1697330E-03 1.333730 at 20iterations 6.8317167E-04 0.1243076 at 30iterations 5.7192061E-05 8.8865757E-03 at 40iterations 5.1585362E-06 7.5149536E-04 at 50iterations finished qdiffx linear iterations at : 03:16:08 total time elapsed so far: 3.110000 # loops : 50 mean,max change (kT/e) : 5.1585362E-06 7.5149536E-04 energy calculations done at 3.110000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.290000 DelPhi exited at 03:16:09 3.290u 0.192s 0:03.81 91.3% 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 Tue Oct 11 2011 at 03:16:09 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: 281 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2704 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.778992 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): -28.59800 26.83100 ymin,ymax (A): -21.78900 38.24500 zmin,zma (A): -32.89200 24.61500 x,y,z range (A): 55.42900 60.03400 57.50700 scale (grids/A): 1.778992 object centre (A): -0.8835001 8.228002 -4.138499 number of atom coordinates read : 2704 total number of charged atoms : 2554 net assigned charge : -4.499988 assigned positive charge : 396.5138 centred at (gu) : 87.59554 85.48550 98.72716 assigned negative charge : -401.0146 centred at (gu) : 87.58000 85.76805 98.83457 start vw surface at 0.1600000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 70466 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28985 grid for indexing accessible points = 1.400000 m= 22895 mr = 44389 m= 2918 mr = 15188 m= 121 mr = 1456 m= 0 mr = 15 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5200000 number of dielectric boundary points 35352 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 211 iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 19933 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) : 0.5929973 object centre at (A) : -0.8835001 8.228002 -4.138499 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.0680341E-02 -1.4967402E-02 midg,1,midg; midg,igrid,midg -1.6024990E-02 -2.9252864E-02 1,midg,midg; igrid,midg,midg -6.6664084E-03 2.7422153E-03 gauss-seidel spectral radius is 0.9984704 estimated iterations to convergence 203 setup time was (sec) 0.8000000 now iterating at: 03:16:10 rms-change max change #iterations 3.784893 181.1174 at 10iterations 1.686528 65.99924 at 20iterations 0.7517710 26.88802 at 30iterations 0.3364984 11.29685 at 40iterations 0.1494683 5.061764 at 50iterations 6.6876724E-02 2.224904 at 60iterations 2.9908402E-02 1.037713 at 70iterations 1.3352327E-02 0.4527645 at 80iterations 5.9652212E-03 0.2069473 at 90iterations 2.6676354E-03 8.9600205E-02 at 100iterations 1.1955629E-03 3.8598299E-02 at 110iterations 5.3387432E-04 1.6594887E-02 at 120iterations finished qdiffx linear iterations at : 03:16:16 total time elapsed so far: 7.300000 # loops : 120 mean,max change (kT/e) : 5.3387432E-04 1.6594887E-02 energy calculations done at 7.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.470000 DelPhi exited at 03:16:17 7.474u 0.246s 0:08.04 95.8% 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 Tue Oct 11 2011 at 03:16:17 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: 281 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2704 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.668488 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): -28.59800 26.83100 ymin,ymax (A): -21.78900 38.24500 zmin,zma (A): -32.89200 24.61500 x,y,z range (A): 55.42900 60.03400 57.50700 scale (grids/A): 2.668488 object centre (A): -0.8835001 8.228002 -4.138499 number of atom coordinates read : 2704 total number of charged atoms : 2554 net assigned charge : -4.499988 assigned positive charge : 396.5138 centred at (gu) : 86.39336 83.22800 103.0906 assigned negative charge : -401.0146 centred at (gu) : 86.36996 83.65196 103.2520 start vw surface at 0.1400000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 163154 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28985 grid for indexing accessible points = 1.400000 m= 75139 mr = 109277 m= 24159 mr = 57595 m= 4717 mr = 17871 m= 442 mr = 3040 m= 12 mr = 203 m= 0 mr = 0 time to grow re-entrant surface = 0.7000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.240000 number of dielectric boundary points 79637 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 6 iepsmp to db, and charging done at 1.380000 number of grid points assigned charge 20428 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) : 1.778992 object centre at (A) : -0.8835001 8.228002 -4.138499 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2373811 -7.6557763E-02 midg,1,midg; midg,igrid,midg -9.5816635E-02 -0.4437886 1,midg,midg; igrid,midg,midg -6.1929848E-02 -8.3431173E-03 gauss-seidel spectral radius is 0.9992399 estimated iterations to convergence 286 setup time was (sec) 1.550000 now iterating at: 03:16:18 rms-change max change #iterations 9.592685 436.7097 at 10iterations 5.708787 147.6723 at 20iterations 3.345343 73.88965 at 30iterations 1.946355 47.09506 at 40iterations 1.124880 27.62851 at 50iterations 0.6480014 15.43820 at 60iterations 0.3731852 7.502529 at 70iterations 0.2133904 4.977539 at 80iterations 0.1225139 2.345341 at 90iterations 7.0063792E-02 1.277733 at 100iterations 3.9998073E-02 0.8572235 at 110iterations 2.2822084E-02 0.4238243 at 120iterations 1.3034884E-02 0.2459564 at 130iterations 7.4211038E-03 0.1338043 at 140iterations 4.2317687E-03 7.7768326E-02 at 150iterations 2.4165004E-03 4.8019409E-02 at 160iterations 1.3753182E-03 2.7148247E-02 at 170iterations 7.8392908E-04 1.4410019E-02 at 180iterations finished qdiffx linear iterations at : 03:16:29 total time elapsed so far: 11.92000 # loops : 180 mean,max change (kT/e) : 7.8392908E-04 1.4410019E-02 energy calculations done at 11.92000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.09000 DelPhi exited at 03:16:29 12.094u 0.210s 0:12.59 97.6% 0+0k 0+0io 0pf+0w