Sat Oct 15 13:37:27 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 Sat Oct 15 2011 at 13:37:27 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2853 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: 0.5940759 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): -17.16000 35.92300 ymin,ymax (A): -64.45500 -4.530000 zmin,zma (A): -2.768000 57.12400 x,y,z range (A): 53.08300 59.92500 59.89200 scale (grids/A): 0.5940759 object centre (A): 9.381500 -34.49250 27.17800 number of atom coordinates read : 2853 total number of charged atoms : 2699 net assigned charge : 3.000014 assigned positive charge : 416.3019 centred at (gu) : 89.30070 89.36851 87.05288 assigned negative charge : -413.3023 centred at (gu) : 89.43812 89.28898 86.96071 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6780 nv = 96 ne = 84 npr = 55812 no. pairs analyzed = 55812 no. exposed pairs = 4309 no. arc points = 31294 no. surface atoms = 1418 nbur = 1435 mkacc time = 8.9999996E-02 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 = 1.484000 m= 352 mr = 2948 m= 2 mr = 21 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2000000 number of dielectric boundary points 4165 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3104 ## 309 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 8485 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.7803751E-09 2.0754520E-09 midg,1,midg; midg,igrid,midg -1.6638319E-09 3.1548613E-09 1,midg,midg; igrid,midg,midg 6.4040466E-09 -2.8150626E-09 gauss-seidel spectral radius is 0.9853776 estimated iterations to convergence 68 setup time was (sec) 0.4300000 now iterating at: 13:37:28 rms-change max change #iterations 0.1060871 18.00869 at 10iterations 8.6671999E-03 1.375615 at 20iterations 7.2284887E-04 0.1160717 at 30iterations 6.7060886E-05 9.9849701E-03 at 40iterations 9.3378885E-06 1.2474060E-03 at 50iterations finished qdiffx linear iterations at : 13:37:33 total time elapsed so far: 3.570000 # loops : 50 mean,max change (kT/e) : 9.3378885E-06 1.2474060E-03 energy calculations done at 3.570000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.700000 DelPhi exited at 13:37:33 3.704u 0.240s 0:06.28 62.7% 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 Sat Oct 15 2011 at 13:37:34 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2853 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: 1.782228 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): -17.16000 35.92300 ymin,ymax (A): -64.45500 -4.530000 zmin,zma (A): -2.768000 57.12400 x,y,z range (A): 53.08300 59.92500 59.89200 scale (grids/A): 1.782228 object centre (A): 9.381500 -34.49250 27.17800 number of atom coordinates read : 2853 total number of charged atoms : 2699 net assigned charge : 3.000014 assigned positive charge : 416.3019 centred at (gu) : 87.90177 88.10504 81.15811 assigned negative charge : -413.3023 centred at (gu) : 88.31397 87.86671 80.88200 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 71873 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31294 grid for indexing accessible points = 1.400000 m= 22711 mr = 43683 m= 3151 mr = 14343 m= 154 mr = 1451 m= 2 mr = 32 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3700000 number of dielectric boundary points 38382 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 236 iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 21022 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) : 0.5940759 object centre at (A) : 9.381500 -34.49250 27.17800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.4551722E-03 4.1604629E-03 midg,1,midg; midg,igrid,midg 1.9932754E-02 3.7357118E-02 1,midg,midg; igrid,midg,midg 1.6904734E-02 -7.0814631E-04 gauss-seidel spectral radius is 0.9984890 estimated iterations to convergence 204 setup time was (sec) 0.6000000 now iterating at: 13:37:34 rms-change max change #iterations 3.856123 165.1137 at 10iterations 1.729979 66.85822 at 20iterations 0.7739459 29.33086 at 30iterations 0.3463982 12.00594 at 40iterations 0.1562645 5.548664 at 50iterations 7.0235826E-02 2.445912 at 60iterations 3.1640787E-02 0.9558277 at 70iterations 1.4211810E-02 0.4573975 at 80iterations 6.3845487E-03 0.2208939 at 90iterations 2.8671494E-03 0.1031933 at 100iterations 1.2868993E-03 4.3059587E-02 at 110iterations 5.7995867E-04 1.8562317E-02 at 120iterations finished qdiffx linear iterations at : 13:37:47 total time elapsed so far: 8.700000 # loops : 120 mean,max change (kT/e) : 5.7995867E-04 1.8562317E-02 energy calculations done at 8.700000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.820000 DelPhi exited at 13:37:48 8.824u 0.245s 0:14.11 64.2% 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 Sat Oct 15 2011 at 13:37:48 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2853 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: 2.673342 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): -17.16000 35.92300 ymin,ymax (A): -64.45500 -4.530000 zmin,zma (A): -2.768000 57.12400 x,y,z range (A): 53.08300 59.92500 59.89200 scale (grids/A): 2.673342 object centre (A): 9.381500 -34.49250 27.17800 number of atom coordinates read : 2853 total number of charged atoms : 2699 net assigned charge : 3.000014 assigned positive charge : 416.3019 centred at (gu) : 86.85266 87.15737 76.73696 assigned negative charge : -413.3023 centred at (gu) : 87.47091 86.79998 76.32288 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 165900 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31294 grid for indexing accessible points = 1.400000 m= 74386 mr = 107915 m= 24301 mr = 55118 m= 5162 mr = 17317 m= 642 mr = 3259 m= 17 mr = 314 m= 0 mr = 4 time to grow re-entrant surface = 0.5400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.000000 number of dielectric boundary points 86481 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 1.140000 number of grid points assigned charge 21584 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) : 1.782228 object centre at (A) : 9.381500 -34.49250 27.17800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.2155496E-02 6.4386263E-02 midg,1,midg; midg,igrid,midg 0.7176844 0.4899442 1,midg,midg; igrid,midg,midg 0.1353903 5.7258569E-02 gauss-seidel spectral radius is 0.9992477 estimated iterations to convergence 288 setup time was (sec) 1.290000 now iterating at: 13:37:49 rms-change max change #iterations 9.803264 298.3787 at 10iterations 5.851213 164.3187 at 20iterations 3.444040 102.0325 at 30iterations 2.008395 48.93089 at 40iterations 1.167531 27.33548 at 50iterations 0.6760718 17.30953 at 60iterations 0.3904201 9.189899 at 70iterations 0.2251732 6.164594 at 80iterations 0.1293187 2.875730 at 90iterations 7.4341968E-02 1.446689 at 100iterations 4.2643618E-02 0.8407421 at 110iterations 2.4438571E-02 0.5739260 at 120iterations 1.4020314E-02 0.3037949 at 130iterations 8.0433581E-03 0.1662903 at 140iterations 4.6017752E-03 9.1228485E-02 at 150iterations 2.6305714E-03 5.9320450E-02 at 160iterations 1.5081123E-03 3.0036926E-02 at 170iterations 8.6201611E-04 1.7343521E-02 at 180iterations finished qdiffx linear iterations at : 13:38:14 total time elapsed so far: 14.07000 # loops : 180 mean,max change (kT/e) : 8.6201611E-04 1.7343521E-02 energy calculations done at 14.07000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.21000 DelPhi exited at 13:38:14 14.211u 0.322s 0:26.70 54.4% 0+0k 0+0io 0pf+0w