Sun Oct 9 19:15:42 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 Sun Oct 9 2011 at 19:15:42 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: 298 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4876 !!! WARNING: HIQ 377 has a net charge of 0.5140 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 0.5576704 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): 2.505000 63.65000 ymin,ymax (A): -7.589000 53.38000 zmin,zma (A): -2.121000 61.71600 x,y,z range (A): 61.14500 60.96900 63.83700 scale (grids/A): 0.5576704 object centre (A): 33.07750 22.89550 29.79750 number of atom coordinates read : 4876 total number of charged atoms : 4748 net assigned charge : 0.6350536 assigned positive charge : 752.0594 centred at (gu) : 88.32751 88.85309 89.33309 assigned negative charge : -751.4296 centred at (gu) : 88.20245 88.86391 89.31082 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 9901 nv = 96 ne = 84 npr = 98421 no. pairs analyzed = 98421 no. exposed pairs = 5623 no. arc points = 38659 no. surface atoms = 1936 nbur = 2940 mkacc time = 0.2500000 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 = 1.540000 m= 468 mr = 5711 m= 0 mr = 16 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5100000 number of dielectric boundary points 4642 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3991 ## 456 charges are in solution ## iepsmp to db, and charging done at 0.6300000 number of grid points assigned charge 13053 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.3000067E-10 4.1110781E-10 midg,1,midg; midg,igrid,midg 3.8281425E-10 -6.1565267E-11 1,midg,midg; igrid,midg,midg -3.1493583E-09 1.4715144E-09 gauss-seidel spectral radius is 0.9835550 estimated iterations to convergence 64 setup time was (sec) 0.8300000 now iterating at: 19:15:43 rms-change max change #iterations 0.1114260 14.92533 at 10iterations 9.9887876E-03 1.416367 at 20iterations 2.7467015E-03 0.3059921 at 30iterations 1.2615703E-03 0.1557655 at 40iterations 6.0522743E-04 7.8179836E-02 at 50iterations finished qdiffx linear iterations at : 19:15:48 total time elapsed so far: 5.440000 # loops : 50 mean,max change (kT/e) : 6.0522743E-04 7.8179836E-02 energy calculations done at 5.440000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.620000 DelPhi exited at 19:15:49 5.625u 0.497s 0:06.38 95.7% 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 Sun Oct 9 2011 at 19:15:49 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: 298 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4876 !!! WARNING: HIQ 377 has a net charge of 0.5140 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 1.673011 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): 2.505000 63.65000 ymin,ymax (A): -7.589000 53.38000 zmin,zma (A): -2.121000 61.71600 x,y,z range (A): 61.14500 60.96900 63.83700 scale (grids/A): 1.673011 object centre (A): 33.07750 22.89550 29.79750 number of atom coordinates read : 4876 total number of charged atoms : 4748 net assigned charge : 0.6350536 assigned positive charge : 752.0594 centred at (gu) : 84.98109 86.55790 87.99772 assigned negative charge : -751.4296 centred at (gu) : 84.60718 86.59180 87.93217 start vw surface at 0.1700000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 111323 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38659 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 38260 mr = 80936 m= 4607 mr = 27702 m= 146 mr = 2474 m= 1 mr = 26 m= 0 mr = 0 time to grow re-entrant surface = 0.5100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.9400000 number of dielectric boundary points 43199 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 370 ## 5 charges are in solution ## iepsmp to db, and charging done at 1.140000 number of grid points assigned charge 36592 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) : 0.5576704 object centre at (A) : 33.07750 22.89550 29.79750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.9669143E-02 -2.7733078E-02 midg,1,midg; midg,igrid,midg 2.0247530E-02 1.1536422E-02 1,midg,midg; igrid,midg,midg -2.4396598E-03 3.6270119E-02 gauss-seidel spectral radius is 0.9984502 estimated iterations to convergence 202 setup time was (sec) 1.360000 now iterating at: 19:15:50 rms-change max change #iterations 4.815952 192.5716 at 10iterations 2.144524 63.25558 at 20iterations 0.9580247 28.20346 at 30iterations 0.4281122 12.43670 at 40iterations 0.1912304 5.302896 at 50iterations 8.6106509E-02 2.447388 at 60iterations 3.9047819E-02 1.095673 at 70iterations 1.8010169E-02 0.5328798 at 80iterations 8.8082859E-03 0.2530060 at 90iterations 4.7960281E-03 0.1386528 at 100iterations 2.9961187E-03 8.0458641E-02 at 110iterations 2.0797583E-03 5.5793762E-02 at 120iterations finished qdiffx linear iterations at : 19:16:03 total time elapsed so far: 13.82000 # loops : 120 mean,max change (kT/e) : 2.0797583E-03 5.5793762E-02 energy calculations done at 13.82000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.11000 DelPhi exited at 19:16:04 14.113u 0.539s 0:14.91 98.1% 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 Sun Oct 9 2011 at 19:16:04 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: 298 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4876 !!! WARNING: HIQ 377 has a net charge of 0.5140 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 2.509516 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): 2.505000 63.65000 ymin,ymax (A): -7.589000 53.38000 zmin,zma (A): -2.121000 61.71600 x,y,z range (A): 61.14500 60.96900 63.83700 scale (grids/A): 2.509516 object centre (A): 33.07750 22.89550 29.79750 number of atom coordinates read : 4876 total number of charged atoms : 4748 net assigned charge : 0.6350536 assigned positive charge : 752.0594 centred at (gu) : 82.47125 84.83666 86.99635 assigned negative charge : -751.4296 centred at (gu) : 81.91074 84.88770 86.89832 start vw surface at 0.1700000 fill in re-entrant regions at 0.6900000 boundary points on vw surface= 258495 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38659 grid for indexing accessible points = 1.400000 m= 129950 mr = 196261 m= 40961 mr = 106447 m= 7524 mr = 31738 m= 665 mr = 5176 m= 17 mr = 363 m= 0 mr = 0 time to grow re-entrant surface = 1.490000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.340000 number of dielectric boundary points 97627 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 18 iepsmp to db, and charging done at 2.520000 number of grid points assigned charge 37953 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) : 1.673011 object centre at (A) : 33.07750 22.89550 29.79750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3404018 -0.7353449 midg,1,midg; midg,igrid,midg 0.1094396 7.3445328E-02 1,midg,midg; igrid,midg,midg 3.8107868E-02 0.5878454 gauss-seidel spectral radius is 0.9992555 estimated iterations to convergence 289 setup time was (sec) 2.760000 now iterating at: 19:16:07 rms-change max change #iterations 12.20454 426.4517 at 10iterations 7.215687 213.2637 at 20iterations 4.237743 96.30164 at 30iterations 2.482701 49.37939 at 40iterations 1.441074 29.25410 at 50iterations 0.8374261 13.78399 at 60iterations 0.4846746 8.526787 at 70iterations 0.2802973 4.753006 at 80iterations 0.1620422 2.806084 at 90iterations 9.3459278E-02 1.649807 at 100iterations 5.4113209E-02 0.8352385 at 110iterations 3.1316314E-02 0.5484600 at 120iterations 1.8233392E-02 0.2910442 at 130iterations 1.0774439E-02 0.1850853 at 140iterations 6.5272306E-03 0.1058655 at 150iterations 4.1337940E-03 7.3791504E-02 at 160iterations 2.7950543E-03 4.9182892E-02 at 170iterations 2.0250804E-03 3.5488129E-02 at 180iterations finished qdiffx linear iterations at : 19:16:28 total time elapsed so far: 23.71000 # loops : 180 mean,max change (kT/e) : 2.0250804E-03 3.5488129E-02 energy calculations done at 23.71000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 23.88000 DelPhi exited at 19:16:28 23.888u 0.584s 0:24.75 98.8% 0+0k 0+0io 0pf+0w