Mon Oct 10 13:55:33 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+sph.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 = amb.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 Mon Oct 10 2011 at 13:55:33 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1694 !!! WARNING: NAP 164 has a net charge of -2.0180 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7266937 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): -6.517000 37.40000 ymin,ymax (A): 1.078000 50.06700 zmin,zma (A): 6.330000 47.41100 x,y,z range (A): 43.91700 48.98900 41.08100 scale (grids/A): 0.7266937 object centre (A): 15.44150 25.57250 26.87050 number of atom coordinates read : 1694 total number of charged atoms : 1557 net assigned charge : -11.51799 assigned positive charge : 250.3892 centred at (gu) : 91.02086 91.15884 90.86884 assigned negative charge : -261.9071 centred at (gu) : 91.01266 91.34900 90.54012 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 6012 nv = 96 ne = 84 npr = 36924 no. pairs analyzed = 36924 no. exposed pairs = 2113 no. arc points = 14831 no. surface atoms = 722 nbur = 972 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 374 mr = 3380 m= 2 mr = 51 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 88 time to turn everything in is 0.2300000 number of dielectric boundary points 2957 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1261 ## 72 charges are in solution ## iepsmp to db, and charging done at 0.3400000 number of grid points assigned charge 6480 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.0917420E-07 6.0174912E-08 midg,1,midg; midg,igrid,midg -2.8470319E-08 -3.3998734E-07 1,midg,midg; igrid,midg,midg -1.2960601E-07 -1.7593700E-07 gauss-seidel spectral radius is 0.9900887 estimated iterations to convergence 82 setup time was (sec) 0.4800000 now iterating at: 13:55:34 rms-change max change #iterations 0.2040746 33.32533 at 10iterations 2.6626019E-02 3.558342 at 20iterations 3.3656741E-03 0.5082150 at 30iterations 4.4252613E-04 6.2156677E-02 at 40iterations 5.7544403E-05 8.1464052E-03 at 50iterations finished qdiffx linear iterations at : 13:55:37 total time elapsed so far: 3.840000 # loops : 50 mean,max change (kT/e) : 5.7544403E-05 8.1464052E-03 energy calculations done at 3.840000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.020000 DelPhi exited at 13:55:38 4.022u 0.244s 0:04.56 93.4% 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 Mon Oct 10 2011 at 13:55:38 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1694 !!! WARNING: NAP 164 has a net charge of -2.0180 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.180081 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): -6.517000 37.40000 ymin,ymax (A): 1.078000 50.06700 zmin,zma (A): 6.330000 47.41100 x,y,z range (A): 43.91700 48.98900 41.08100 scale (grids/A): 2.180081 object centre (A): 15.44150 25.57250 26.87050 number of atom coordinates read : 1694 total number of charged atoms : 1557 net assigned charge : -11.51799 assigned positive charge : 250.3892 centred at (gu) : 93.06276 93.47666 92.60655 assigned negative charge : -261.9071 centred at (gu) : 93.03799 94.04721 91.62053 start vw surface at 0.1500000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 63322 reading accessible surface arcs data from file ARCDAT no. of arc points read = 14831 grid for indexing accessible points = 1.400000 m= 25155 mr = 43780 m= 4659 mr = 19249 m= 331 mr = 3161 m= 9 mr = 135 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 2875 time to turn everything in is 0.5900000 number of dielectric boundary points 27151 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 45 iepsmp to db, and charging done at 0.7200000 number of grid points assigned charge 12404 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) : 0.7266937 object centre at (A) : 15.44150 25.57250 26.87050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.7922883E-02 2.5792656E-02 midg,1,midg; midg,igrid,midg -5.5224597E-03 -8.2624756E-02 1,midg,midg; igrid,midg,midg -5.5231500E-02 -7.7326603E-02 gauss-seidel spectral radius is 0.9988447 estimated iterations to convergence 233 setup time was (sec) 0.9100000 now iterating at: 13:55:39 rms-change max change #iterations 4.452221 188.1309 at 10iterations 2.205328 83.66446 at 20iterations 1.093974 36.45268 at 30iterations 0.5438057 19.13602 at 40iterations 0.2708617 8.849906 at 50iterations 0.1346800 4.259598 at 60iterations 6.6887185E-02 2.028284 at 70iterations 3.3422705E-02 1.105171 at 80iterations 1.6577017E-02 0.5398750 at 90iterations 8.2207592E-03 0.2396240 at 100iterations 4.0849117E-03 0.1317520 at 110iterations 2.0400034E-03 6.2066913E-02 at 120iterations finished qdiffx linear iterations at : 13:55:47 total time elapsed so far: 9.170000 # loops : 120 mean,max change (kT/e) : 2.0400034E-03 6.2066913E-02 energy calculations done at 9.170000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.350000 DelPhi exited at 13:55:48 9.355u 0.257s 0:10.19 94.2% 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 Mon Oct 10 2011 at 13:55:48 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1694 !!! WARNING: NAP 164 has a net charge of -2.0180 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 3.270122 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): -6.517000 37.40000 ymin,ymax (A): 1.078000 50.06700 zmin,zma (A): 6.330000 47.41100 x,y,z range (A): 43.91700 48.98900 41.08100 scale (grids/A): 3.270122 object centre (A): 15.44150 25.57250 26.87050 number of atom coordinates read : 1694 total number of charged atoms : 1557 net assigned charge : -11.51799 assigned positive charge : 250.3892 centred at (gu) : 94.59396 95.21497 93.90994 assigned negative charge : -261.9071 centred at (gu) : 94.55707 96.07088 92.43081 start vw surface at 0.1300000 fill in re-entrant regions at 0.8600000 boundary points on vw surface= 145947 reading accessible surface arcs data from file ARCDAT no. of arc points read = 14831 grid for indexing accessible points = 1.400000 m= 77406 mr = 105379 m= 32163 mr = 64617 m= 8862 mr = 26772 m= 1463 mr = 6901 m= 141 mr = 1014 m= 5 mr = 85 m= 0 mr = 2 time to grow re-entrant surface = 0.7800000 no. cavity mid-points inaccessible to solvent = 9892 time to turn everything in is 1.750000 number of dielectric boundary points 61217 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.890000 number of grid points assigned charge 12456 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) : 2.180081 object centre at (A) : 15.44150 25.57250 26.87050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.4515253 0.3157138 midg,1,midg; midg,igrid,midg -3.3904504E-02 -0.7080071 1,midg,midg; igrid,midg,midg -0.3855435 -0.5712536 gauss-seidel spectral radius is 0.9992935 estimated iterations to convergence 297 setup time was (sec) 2.080000 now iterating at: 13:55:50 rms-change max change #iterations 9.796334 434.2427 at 10iterations 5.704755 121.2872 at 20iterations 3.332940 65.23147 at 30iterations 1.939567 38.60666 at 40iterations 1.129097 21.99860 at 50iterations 0.6574066 12.04035 at 60iterations 0.3824975 7.282166 at 70iterations 0.2225916 4.220908 at 80iterations 0.1295717 3.000034 at 90iterations 7.5029142E-02 1.402305 at 100iterations 4.3744441E-02 0.7823715 at 110iterations 2.5414519E-02 0.4592438 at 120iterations 1.4797805E-02 0.2766094 at 130iterations 8.5850749E-03 0.1509746 at 140iterations 4.9890289E-03 8.9035034E-02 at 150iterations 2.8934879E-03 5.2261353E-02 at 160iterations 1.6891797E-03 2.9258728E-02 at 170iterations 9.8110142E-04 2.0175934E-02 at 180iterations finished qdiffx linear iterations at : 13:56:03 total time elapsed so far: 15.08000 # loops : 180 mean,max change (kT/e) : 9.8110142E-04 2.0175934E-02 energy calculations done at 15.08000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.26000 DelPhi exited at 13:56:04 15.261u 0.286s 0:16.32 95.2% 0+0k 0+0io 0pf+0w