Mon Oct 10 14:00:44 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 Mon Oct 10 2011 at 14:00:45 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: 313 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2825 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: 0.5467418 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): 4.639000 59.53100 ymin,ymax (A): -9.663000 55.45000 zmin,zma (A): 80.11100 137.2780 x,y,z range (A): 54.89200 65.11300 57.16700 scale (grids/A): 0.5467418 object centre (A): 32.08500 22.89350 108.6945 number of atom coordinates read : 2825 total number of charged atoms : 2688 net assigned charge : 2.000011 assigned positive charge : 437.3935 centred at (gu) : 91.80678 89.03313 90.58388 assigned negative charge : -435.3943 centred at (gu) : 91.73248 89.01439 90.46338 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 5569 nv = 96 ne = 84 npr = 55298 no. pairs analyzed = 55298 no. exposed pairs = 3885 no. arc points = 28181 no. surface atoms = 1302 nbur = 1523 mkacc time = 0.1000000 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 = 1.568000 m= 225 mr = 2659 m= 0 mr = 11 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2100000 number of dielectric boundary points 3124 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2791 ## 361 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 7250 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.0467081E-10 1.0479659E-09 midg,1,midg; midg,igrid,midg -1.5654781E-11 1.8877194E-10 1,midg,midg; igrid,midg,midg -2.4412639E-10 9.5331054E-10 gauss-seidel spectral radius is 0.9827478 estimated iterations to convergence 63 setup time was (sec) 0.4100000 now iterating at: 14:00:46 rms-change max change #iterations 7.2686069E-02 11.48682 at 10iterations 4.8386483E-03 0.8391190 at 20iterations 3.7848364E-04 6.3873291E-02 at 30iterations 4.1778629E-05 8.0947876E-03 at 40iterations 6.6660573E-06 1.3170242E-03 at 50iterations finished qdiffx linear iterations at : 14:00:49 total time elapsed so far: 3.290000 # loops : 50 mean,max change (kT/e) : 6.6660573E-06 1.3170242E-03 energy calculations done at 3.290000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.430000 DelPhi exited at 14:00:50 3.433u 0.168s 0:05.28 67.9% 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 14:00:50 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: 313 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2825 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: 1.640226 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): 4.639000 59.53100 ymin,ymax (A): -9.663000 55.45000 zmin,zma (A): 80.11100 137.2780 x,y,z range (A): 54.89200 65.11300 57.16700 scale (grids/A): 1.640226 object centre (A): 32.08500 22.89350 108.6945 number of atom coordinates read : 2825 total number of charged atoms : 2688 net assigned charge : 2.000011 assigned positive charge : 437.3935 centred at (gu) : 95.41956 87.09881 91.75079 assigned negative charge : -435.3943 centred at (gu) : 95.19733 87.04261 91.39002 start vw surface at 0.1100000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 61022 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28181 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 18620 mr = 39479 m= 2141 mr = 12398 m= 82 mr = 1088 m= 3 mr = 10 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 260 time to turn everything in is 0.3300000 number of dielectric boundary points 28893 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 317 ## 5 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 20604 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) : 0.5467418 object centre at (A) : 32.08500 22.89350 108.6945 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.1012560E-03 1.1689248E-02 midg,1,midg; midg,igrid,midg 1.0766108E-03 4.7685116E-04 1,midg,midg; igrid,midg,midg -7.7799093E-03 -1.7956684E-03 gauss-seidel spectral radius is 0.9981956 estimated iterations to convergence 187 setup time was (sec) 0.5400000 now iterating at: 14:00:51 rms-change max change #iterations 3.301378 183.9254 at 10iterations 1.372907 55.36145 at 20iterations 0.5717764 23.60857 at 30iterations 0.2385652 9.860394 at 40iterations 9.9811271E-02 3.481465 at 50iterations 4.1561112E-02 1.507432 at 60iterations 1.7417802E-02 0.6419877 at 70iterations 7.2681280E-03 0.2721558 at 80iterations 3.0347265E-03 0.1054497 at 90iterations 1.2746388E-03 5.1013947E-02 at 100iterations 5.3394120E-04 2.1636963E-02 at 110iterations 2.2437841E-04 8.7289810E-03 at 120iterations finished qdiffx linear iterations at : 14:00:58 total time elapsed so far: 7.570000 # loops : 120 mean,max change (kT/e) : 2.2437841E-04 8.7289810E-03 energy calculations done at 7.570000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.690000 DelPhi exited at 14:00:59 7.696u 0.200s 0:09.07 86.9% 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 14:01:00 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: 313 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2825 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: 2.460338 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): 4.639000 59.53100 ymin,ymax (A): -9.663000 55.45000 zmin,zma (A): 80.11100 137.2780 x,y,z range (A): 54.89200 65.11300 57.16700 scale (grids/A): 2.460338 object centre (A): 32.08500 22.89350 108.6945 number of atom coordinates read : 2825 total number of charged atoms : 2688 net assigned charge : 2.000011 assigned positive charge : 437.3935 centred at (gu) : 98.12935 85.64800 92.62613 assigned negative charge : -435.3943 centred at (gu) : 97.79594 85.56387 92.08500 start vw surface at 0.1000000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 141764 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28181 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 63714 mr = 97402 m= 18790 mr = 49071 m= 3445 mr = 13773 m= 292 mr = 2265 m= 8 mr = 146 m= 0 mr = 0 time to grow re-entrant surface = 0.4100000 no. cavity mid-points inaccessible to solvent = 820 time to turn everything in is 0.7600000 number of dielectric boundary points 65356 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 29 iepsmp to db, and charging done at 0.8600000 number of grid points assigned charge 21476 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) : 1.640226 object centre at (A) : 32.08500 22.89350 108.6945 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.8794417E-02 9.6660376E-02 midg,1,midg; midg,igrid,midg -3.5334919E-02 -3.9323311E-02 1,midg,midg; igrid,midg,midg -8.6482376E-02 -0.1406943 gauss-seidel spectral radius is 0.9991388 estimated iterations to convergence 269 setup time was (sec) 1.000000 now iterating at: 14:01:02 rms-change max change #iterations 8.618934 312.8843 at 10iterations 4.815191 121.8176 at 20iterations 2.682776 61.20981 at 30iterations 1.488459 32.53384 at 40iterations 0.8234624 17.62338 at 50iterations 0.4541394 11.12566 at 60iterations 0.2504759 5.298698 at 70iterations 0.1378977 2.953322 at 80iterations 7.6088913E-02 1.679737 at 90iterations 4.1816916E-02 0.9749393 at 100iterations 2.2955243E-02 0.4780846 at 110iterations 1.2632833E-02 0.2798836 at 120iterations 6.9317571E-03 0.1455584 at 130iterations 3.8163799E-03 8.4899902E-02 at 140iterations 2.0976758E-03 4.3924332E-02 at 150iterations 1.1554445E-03 2.5875092E-02 at 160iterations 6.3579960E-04 1.4177322E-02 at 170iterations 3.5047613E-04 7.5225830E-03 at 180iterations finished qdiffx linear iterations at : 14:01:13 total time elapsed so far: 12.15000 # loops : 180 mean,max change (kT/e) : 3.5047613E-04 7.5225830E-03 energy calculations done at 12.15000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.28000 DelPhi exited at 14:01:13 12.280u 0.209s 0:13.09 95.3% 0+0k 0+0io 0pf+0w