Sat Oct 15 13:49:14 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 Sat Oct 15 2011 at 13:49:15 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3188 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: 0.5213521 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): 33.88000 89.18300 ymin,ymax (A): -8.168000 47.12400 zmin,zma (A): 75.14400 143.4280 x,y,z range (A): 55.30300 55.29200 68.28400 scale (grids/A): 0.5213521 object centre (A): 61.53150 19.47800 109.2860 number of atom coordinates read : 3188 total number of charged atoms : 3049 net assigned charge : 7.000029 assigned positive charge : 473.6905 centred at (gu) : 90.57281 90.22369 90.34087 assigned negative charge : -466.6917 centred at (gu) : 90.63382 90.18362 90.14645 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 5766 nv = 96 ne = 84 npr = 61801 no. pairs analyzed = 61801 no. exposed pairs = 4472 no. arc points = 31634 no. surface atoms = 1478 nbur = 1710 mkacc time = 9.9999994E-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 = 1.652000 m= 232 mr = 2725 m= 0 mr = 10 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2200000 number of dielectric boundary points 3263 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3182 ## 475 charges are in solution ## iepsmp to db, and charging done at 0.2900000 number of grid points assigned charge 7634 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.3982103E-10 7.2416267E-10 midg,1,midg; midg,igrid,midg 4.8730100E-11 2.8005062E-10 1,midg,midg; igrid,midg,midg 2.7589664E-10 -7.3068262E-12 gauss-seidel spectral radius is 0.9810834 estimated iterations to convergence 60 setup time was (sec) 0.4300000 now iterating at: 13:49:15 rms-change max change #iterations 5.9909020E-02 9.892652 at 10iterations 3.5248320E-03 0.6631889 at 20iterations 2.0855824E-04 3.7269592E-02 at 30iterations 1.2500564E-05 2.2621155E-03 at 40iterations 8.4994565E-07 1.2779236E-04 at 50iterations finished qdiffx linear iterations at : 13:49:21 total time elapsed so far: 3.590000 # loops : 50 mean,max change (kT/e) : 8.4994565E-07 1.2779236E-04 energy calculations done at 3.590000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.720000 DelPhi exited at 13:49:21 3.722u 0.222s 0:06.66 59.1% 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 Sat Oct 15 2011 at 13:49:21 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3188 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: 1.564056 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): 33.88000 89.18300 ymin,ymax (A): -8.168000 47.12400 zmin,zma (A): 75.14400 143.4280 x,y,z range (A): 55.30300 55.29200 68.28400 scale (grids/A): 1.564056 object centre (A): 61.53150 19.47800 109.2860 number of atom coordinates read : 3188 total number of charged atoms : 3049 net assigned charge : 7.000029 assigned positive charge : 473.6905 centred at (gu) : 91.71746 90.67020 91.02147 assigned negative charge : -466.6917 centred at (gu) : 91.90080 90.55046 90.43904 start vw surface at 0.1000000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 64293 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31634 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 17978 mr = 41441 m= 1697 mr = 11467 m= 56 mr = 659 m= 0 mr = 1 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 969 time to turn everything in is 0.3600000 number of dielectric boundary points 30456 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 408 ## 7 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 23108 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) : 0.5213521 object centre at (A) : 61.53150 19.47800 109.2860 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.0247886E-03 1.5238235E-02 midg,1,midg; midg,igrid,midg 6.6414075E-03 9.2557184E-03 1,midg,midg; igrid,midg,midg 5.1658065E-03 -5.6083086E-03 gauss-seidel spectral radius is 0.9980575 estimated iterations to convergence 180 setup time was (sec) 0.6000000 now iterating at: 13:49:22 rms-change max change #iterations 3.085468 167.8912 at 10iterations 1.251019 55.30289 at 20iterations 0.5040037 20.28766 at 30iterations 0.2037638 7.558661 at 40iterations 8.2140863E-02 2.954065 at 50iterations 3.3180639E-02 1.223804 at 60iterations 1.3437790E-02 0.5555153 at 70iterations 5.4405960E-03 0.1894760 at 80iterations 2.1925243E-03 8.3213806E-02 at 90iterations 8.8772253E-04 3.5581589E-02 at 100iterations 3.5893993E-04 1.3504028E-02 at 110iterations 1.4508744E-04 5.5313110E-03 at 120iterations finished qdiffx linear iterations at : 13:49:34 total time elapsed so far: 8.220000 # loops : 120 mean,max change (kT/e) : 1.4508744E-04 5.5313110E-03 energy calculations done at 8.220000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.350000 DelPhi exited at 13:49:34 8.356u 0.243s 0:13.24 64.8% 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 Sat Oct 15 2011 at 13:49:35 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3188 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.346084 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): 33.88000 89.18300 ymin,ymax (A): -8.168000 47.12400 zmin,zma (A): 75.14400 143.4280 x,y,z range (A): 55.30300 55.29200 68.28400 scale (grids/A): 2.346084 object centre (A): 61.53150 19.47800 109.2860 number of atom coordinates read : 3188 total number of charged atoms : 3049 net assigned charge : 7.000029 assigned positive charge : 473.6905 centred at (gu) : 92.57578 91.00507 91.53201 assigned negative charge : -466.6917 centred at (gu) : 92.85111 90.82559 90.65839 start vw surface at 0.1000000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 149525 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31634 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 63961 mr = 102439 m= 16395 mr = 48394 m= 2415 mr = 11416 m= 158 mr = 1386 m= 5 mr = 38 m= 0 mr = 0 time to grow re-entrant surface = 0.4200000 no. cavity mid-points inaccessible to solvent = 3320 time to turn everything in is 0.8000000 number of dielectric boundary points 68786 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 32 iepsmp to db, and charging done at 0.8900000 number of grid points assigned charge 24330 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) : 1.564056 object centre at (A) : 61.53150 19.47800 109.2860 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1293900 0.2093414 midg,1,midg; midg,igrid,midg 0.1273127 0.1394673 1,midg,midg; igrid,midg,midg 8.4446311E-02 -9.8525308E-02 gauss-seidel spectral radius is 0.9991141 estimated iterations to convergence 265 setup time was (sec) 1.030000 now iterating at: 13:49:38 rms-change max change #iterations 8.338639 323.0595 at 10iterations 4.657528 122.4124 at 20iterations 2.590849 74.06434 at 30iterations 1.429672 37.68216 at 40iterations 0.7903163 17.91640 at 50iterations 0.4341939 9.790678 at 60iterations 0.2380342 5.623375 at 70iterations 0.1300865 3.208747 at 80iterations 7.1184486E-02 1.720646 at 90iterations 3.8951371E-02 0.8331099 at 100iterations 2.1223994E-02 0.4862251 at 110iterations 1.1570303E-02 0.2568159 at 120iterations 6.3181217E-03 0.1544628 at 130iterations 3.4414602E-03 7.0523262E-02 at 140iterations 1.8749954E-03 4.1217804E-02 at 150iterations 1.0237022E-03 2.2994041E-02 at 160iterations 5.5673032E-04 1.1322021E-02 at 170iterations 3.0380706E-04 6.3838959E-03 at 180iterations finished qdiffx linear iterations at : 13:50:03 total time elapsed so far: 13.69000 # loops : 180 mean,max change (kT/e) : 3.0380706E-04 6.3838959E-03 energy calculations done at 13.69000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.83000 DelPhi exited at 13:50:04 13.828u 0.277s 0:28.59 49.2% 0+0k 0+0io 0pf+0w