Tue Oct 11 05:58:29 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 05:58:29 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: 297 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2073 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7399709 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): -17.95700 30.15300 ymin,ymax (A): -11.47900 30.56100 zmin,zma (A): -8.546000 38.11900 x,y,z range (A): 48.11000 42.04000 46.66500 scale (grids/A): 0.7399709 object centre (A): 6.098001 9.541000 14.78650 number of atom coordinates read : 2073 total number of charged atoms : 1943 net assigned charge : 6.039010 assigned positive charge : 317.7461 centred at (gu) : 90.08076 89.65794 91.07138 assigned negative charge : -311.7072 centred at (gu) : 89.99981 89.57486 90.95272 start vw surface at 7.9999998E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 7808 nv = 96 ne = 84 npr = 41863 no. pairs analyzed = 41863 no. exposed pairs = 2536 no. arc points = 17150 no. surface atoms = 864 nbur = 1209 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 569 mr = 4569 m= 1 mr = 132 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 47 time to turn everything in is 0.1700000 number of dielectric boundary points 3677 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1538 ## 149 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 8233 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -9.7613908E-09 2.7041534E-07 midg,1,midg; midg,igrid,midg 2.3563681E-08 1.7528228E-07 1,midg,midg; igrid,midg,midg 2.4364761E-08 1.8742368E-07 gauss-seidel spectral radius is 0.9904717 estimated iterations to convergence 83 setup time was (sec) 0.3700000 now iterating at: 05:58:30 rms-change max change #iterations 0.2437583 30.66714 at 10iterations 3.3427596E-02 4.794878 at 20iterations 4.7776522E-03 0.6312103 at 30iterations 7.8840210E-04 0.1066046 at 40iterations 1.7938705E-04 1.8871307E-02 at 50iterations finished qdiffx linear iterations at : 05:58:33 total time elapsed so far: 3.360000 # loops : 50 mean,max change (kT/e) : 1.7938705E-04 1.8871307E-02 energy calculations done at 3.360000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.490000 DelPhi exited at 05:58:33 3.493u 0.192s 0:04.01 91.7% 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 Tue Oct 11 2011 at 05:58:33 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: 297 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2073 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.219913 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): -17.95700 30.15300 ymin,ymax (A): -11.47900 30.56100 zmin,zma (A): -8.546000 38.11900 x,y,z range (A): 48.11000 42.04000 46.66500 scale (grids/A): 2.219913 object centre (A): 6.098001 9.541000 14.78650 number of atom coordinates read : 2073 total number of charged atoms : 1943 net assigned charge : 6.039010 assigned positive charge : 317.7461 centred at (gu) : 90.24232 88.97387 93.21424 assigned negative charge : -311.7072 centred at (gu) : 89.99961 88.72459 92.85817 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 81734 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17150 grid for indexing accessible points = 1.400000 m= 35076 mr = 58549 m= 7705 mr = 27335 m= 861 mr = 5429 m= 32 mr = 486 m= 0 mr = 8 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 1234 time to turn everything in is 0.4300000 number of dielectric boundary points 33601 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 55 iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 15474 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) : 0.7399709 object centre at (A) : 6.098001 9.541000 14.78650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.9795218E-02 5.4503057E-02 midg,1,midg; midg,igrid,midg 3.0259514E-02 2.8896023E-02 1,midg,midg; igrid,midg,midg 4.0680829E-02 3.7140038E-02 gauss-seidel spectral radius is 0.9989151 estimated iterations to convergence 240 setup time was (sec) 0.6600000 now iterating at: 05:58:34 rms-change max change #iterations 5.049455 183.9608 at 10iterations 2.562654 96.89676 at 20iterations 1.305686 40.48897 at 30iterations 0.6634992 18.67947 at 40iterations 0.3383011 10.99565 at 50iterations 0.1727509 4.965343 at 60iterations 8.7673299E-02 2.543285 at 70iterations 4.4905290E-02 1.227522 at 80iterations 2.2958748E-02 0.6165197 at 90iterations 1.1834551E-02 0.3360825 at 100iterations 6.0840510E-03 0.1687088 at 110iterations 3.1867709E-03 9.3116760E-02 at 120iterations finished qdiffx linear iterations at : 05:58:42 total time elapsed so far: 8.120000 # loops : 120 mean,max change (kT/e) : 3.1867709E-03 9.3116760E-02 energy calculations done at 8.120000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.240000 DelPhi exited at 05:58:42 8.247u 0.235s 0:08.76 96.6% 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 05:58:42 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: 297 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2073 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.329869 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): -17.95700 30.15300 ymin,ymax (A): -11.47900 30.56100 zmin,zma (A): -8.546000 38.11900 x,y,z range (A): 48.11000 42.04000 46.66500 scale (grids/A): 3.329869 object centre (A): 6.098001 9.541000 14.78650 number of atom coordinates read : 2073 total number of charged atoms : 1943 net assigned charge : 6.039010 assigned positive charge : 317.7461 centred at (gu) : 90.36354 88.46071 94.82140 assigned negative charge : -311.7072 centred at (gu) : 89.99939 88.08688 94.28718 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 188171 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17150 grid for indexing accessible points = 1.400000 m= 106437 mr = 140683 m= 47033 mr = 89653 m= 14973 mr = 39470 m= 3348 mr = 12024 m= 511 mr = 2553 m= 34 mr = 367 m= 0 mr = 22 time to grow re-entrant surface = 0.7000000 no. cavity mid-points inaccessible to solvent = 4493 time to turn everything in is 1.340000 number of dielectric boundary points 75735 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.430000 number of grid points assigned charge 15544 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) : 2.219913 object centre at (A) : 6.098001 9.541000 14.78650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.5470976 0.5025496 midg,1,midg; midg,igrid,midg 0.2667539 0.1431236 1,midg,midg; igrid,midg,midg 0.2228979 0.1543449 gauss-seidel spectral radius is 0.9993186 estimated iterations to convergence 302 setup time was (sec) 1.590000 now iterating at: 05:58:44 rms-change max change #iterations 10.92607 288.6693 at 10iterations 6.530671 143.3826 at 20iterations 3.882584 76.44228 at 30iterations 2.314981 40.53030 at 40iterations 1.374657 24.16756 at 50iterations 0.8145172 14.62481 at 60iterations 0.4821484 8.954956 at 70iterations 0.2854861 5.028229 at 80iterations 0.1686559 2.913400 at 90iterations 9.9966936E-02 1.784122 at 100iterations 5.9239917E-02 1.146885 at 110iterations 3.5223033E-02 0.5755196 at 120iterations 2.1053126E-02 0.3745327 at 130iterations 1.2806236E-02 0.2555237 at 140iterations 7.9629645E-03 0.1457214 at 150iterations 5.1354961E-03 9.8018646E-02 at 160iterations 3.4781874E-03 6.4481735E-02 at 170iterations 2.5037101E-03 4.5806885E-02 at 180iterations finished qdiffx linear iterations at : 05:58:56 total time elapsed so far: 13.77000 # loops : 180 mean,max change (kT/e) : 2.5037101E-03 4.5806885E-02 energy calculations done at 13.77000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.90000 DelPhi exited at 05:58:57 13.906u 0.228s 0:14.45 97.7% 0+0k 0+0io 0pf+0w